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Volume 2021
2021
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EISSN 1758-0463

Volume 2021, 2021

HIR V2: a human interactome resource for the biological interpretation of differentially expressed genes via gene set linkage analysis
Wen-Ping Guo and others
Database, Volume 2021, 2021, baab009, https://doi.org/10.1093/database/baab009
UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase–substrate interactions
Zhongyan Li and others
Database, Volume 2021, 2021, baab010, https://doi.org/10.1093/database/baab010
Automatization and self-maintenance of the O-GlcNAcome catalog: a smart scientific database
Florian Malard and others
Database, Volume 2021, 2021, baab039, https://doi.org/10.1093/database/baab039
Web tools to perform long non-coding RNAs analysis in oncology research
Shixing Gu and others
Database, Volume 2021, 2021, baab047, https://doi.org/10.1093/database/baab047
circExp database: an online transcriptome platform for human circRNA expressions in cancers
Min Zhao and others
Database, Volume 2021, 2021, baab045, https://doi.org/10.1093/database/baab045
A nomenclature for echinoderm genes
Thomas R Beatman and others
Database, Volume 2021, 2021, baab052, https://doi.org/10.1093/database/baab052
Nabe: an energetic database of amino acid mutations in protein–nucleic acid binding interfaces
Junyi Liu and others
Database, Volume 2021, 2021, baab050, https://doi.org/10.1093/database/baab050
A PostgreSQL Tripal solution for large-scale genotypic and phenotypic data
Lacey-Anne Sanderson and others
Database, Volume 2021, 2021, baab051, https://doi.org/10.1093/database/baab051
lncExplore: a database of pan-cancer analysis and systematic functional annotation for lncRNAs from RNA-sequencing data
Yi-Wei Lee and others
Database, Volume 2021, 2021, baab053, https://doi.org/10.1093/database/baab053
Peptipedia: a user-friendly web application and a comprehensive database for peptide research supported by Machine Learning approach
Cristofer Quiroz and others
Database, Volume 2021, 2021, baab055, https://doi.org/10.1093/database/baab055
Food Enzyme Database (FEDA): a web application gathering information about food enzyme preparations available on the European market
Marie Deckers and others
Database, Volume 2021, 2021, baab060, https://doi.org/10.1093/database/baab060
HBFP: a new repository for human body fluid proteome
Dan Shao and others
Database, Volume 2021, 2021, baab065, https://doi.org/10.1093/database/baab065
The World Spider Trait database: a centralized global open repository for curated data on spider traits
Stano Pekár and others
Database, Volume 2021, 2021, baab064, https://doi.org/10.1093/database/baab064
https://botryosphaeriales.org/, an online platform for up-to-date classification and account of taxa of Botryosphaeriales
N a Wu and others
Database, Volume 2021, 2021, baab061, https://doi.org/10.1093/database/baab061
Mining drug–target and drug–adverse drug reaction databases to identify target–adverse drug reaction relationships
Cristiano Galletti and others
Database, Volume 2021, 2021, baab068, https://doi.org/10.1093/database/baab068
MMV-db: vaccinomics and RNA-based therapeutics database for infectious hemorrhagic fever-causing mammarenaviruses
Taimoor Khan and others
Database, Volume 2021, 2021, baab063, https://doi.org/10.1093/database/baab063
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies
Rebecca Jackson and others
Database, Volume 2021, 2021, baab069, https://doi.org/10.1093/database/baab069
Gene Ontology curation of the blood–brain barrier to improve the analysis of Alzheimer’s and other neurological diseases
Shirin C C Saverimuttu and others
Database, Volume 2021, 2021, baab067, https://doi.org/10.1093/database/baab067
JAMIR-eQTL: Japanese genome-wide identification of microRNA expression quantitative trait loci across dementia types
Shintaro Akiyama and others
Database, Volume 2021, 2021, baab072, https://doi.org/10.1093/database/baab072
At-C-RNA database, a one-stop source for information on circRNAs in Arabidopsis thaliana in a unified format
Katarzyna Nowis and others
Database, Volume 2021, 2021, baab074, https://doi.org/10.1093/database/baab074
Prototheca-ID: a web-based application for molecular identification of Prototheca species
Mikołaj Dziurzyński and others
Database, Volume 2021, 2021, baab073, https://doi.org/10.1093/database/baab073
HFIP: an integrated multi-omics data and knowledge platform for the precision medicine of heart failure
Jing Wu and others
Database, Volume 2021, 2021, baab076, https://doi.org/10.1093/database/baab076
DCMP: database of cancer mutant protein domains
Isaac Arnold Emerson and Kiran Kumar Chitluri
Database, Volume 2021, 2021, baab066, https://doi.org/10.1093/database/baab066
Corrigendum to: the SNPcurator: literature mining of enriched SNP-disease associations
Noha S Tawfik and Marco R Spruit
Database, Volume 2021, 2021, baab070, https://doi.org/10.1093/database/baab070
Corrigendum to: QSDB—a graphical Quorum Sensing Database
Karsten Klein and others
Database, Volume 2021, 2021, baab071, https://doi.org/10.1093/database/baab071
iCAV: an integrative database of cancer-associated viruses
Bo Liu and others
Database, Volume 2021, 2021, baab079, https://doi.org/10.1093/database/baab079
The United States Swine Pathogen Database: integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine
Tavis K Anderson and others
Database, Volume 2021, 2021, baab078, https://doi.org/10.1093/database/baab078
https://www.fungiofpakistan.com: a continuously updated online database of fungi in Pakistan
Mubashar Raza and others
Database, Volume 2021, 2021, baab080, https://doi.org/10.1093/database/baab080
The first comprehensive database of germline pathogenic variants in East Asian cancer patients
Xiaoshun Shi and others
Database, Volume 2021, 2021, baab075, https://doi.org/10.1093/database/baab075

Original Articles

HGFDB: a collective database of helmeted guinea fowl genomics
Xuzhen Li and others
Database, Volume 2021, 2021, baaa116, https://doi.org/10.1093/database/baaa116
Large-scale regulatory and signaling network assembly through linked open data
M Lefebvre and others
Database, Volume 2021, 2021, baaa113, https://doi.org/10.1093/database/baaa113
Converting disease maps into heavyweight ontologies: general methodology and application to Alzheimer’s disease
Vincent Henry and others
Database, Volume 2021, 2021, baab004, https://doi.org/10.1093/database/baab004
Extraction of causal relations based on SBEL and BERT model
Yifan Shao and others
Database, Volume 2021, 2021, baab005, https://doi.org/10.1093/database/baab005
Curation of over 10 000 transcriptomic studies to enable data reuse
Nathaniel Lim and others
Database, Volume 2021, 2021, baab006, https://doi.org/10.1093/database/baab006
CMBD: a manually curated cancer metabolic biomarker knowledge database
Jing Chen and others
Database, Volume 2021, 2021, baaa094, https://doi.org/10.1093/database/baaa094
Development of a biomarker database toward performing disease classification and finding disease interrelations
Shaikh Farhad Hossain and others
Database, Volume 2021, 2021, baab011, https://doi.org/10.1093/database/baab011
An immunologically friendly classification of non-peptidic ligands
Lindy Edwards and others
Database, Volume 2021, 2021, baab014, https://doi.org/10.1093/database/baab014
Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning
Eryk Kropiwnicki and others
Database, Volume 2021, 2021, baab017, https://doi.org/10.1093/database/baab017
Wormicloud: a new text summarization tool based on word clouds to explore the C. elegans literature
Valerio Arnaboldi and others
Database, Volume 2021, 2021, baab015, https://doi.org/10.1093/database/baab015
APICURON: a database to credit and acknowledge the work of biocurators
András Hatos and others
Database, Volume 2021, 2021, baab019, https://doi.org/10.1093/database/baab019
Tripal MegaSearch: a tool for interactive and customizable query and download of big data
Sook Jung and others
Database, Volume 2021, 2021, baab023, https://doi.org/10.1093/database/baab023
Increasing metadata coverage of SRA BioSample entries using deep learning–based named entity recognition
Adam Klie and others
Database, Volume 2021, 2021, baab021, https://doi.org/10.1093/database/baab021
CANNUSE, a database of traditional Cannabis uses—an opportunity for new research
Manica Balant and others
Database, Volume 2021, 2021, baab024, https://doi.org/10.1093/database/baab024
Human IRES Atlas: an integrative platform for studying IRES-driven translational regulation in humans
Tzu-Hsien Yang and others
Database, Volume 2021, 2021, baab025, https://doi.org/10.1093/database/baab025
COVIDOUTCOME—estimating COVID severity based on mutation signatures in the SARS-CoV-2 genome
Ádám Nagy and others
Database, Volume 2021, 2021, baab020, https://doi.org/10.1093/database/baab020
covid19census: U.S. and Italy COVID-19 metrics and other epidemiological data
Claudio Zanettini and others
Database, Volume 2021, 2021, baab027, https://doi.org/10.1093/database/baab027
Challenges for FAIR-compliant description and comparison of crop phenotype data with standardized controlled vocabularies
Liliana Andrés-Hernández and others
Database, Volume 2021, 2021, baab028, https://doi.org/10.1093/database/baab028
Application of beta and gamma carbonic anhydrase sequences as tools for identification of bacterial contamination in the whole genome sequence of inbred Wuzhishan minipig (Sus scrofa) annotated in databases
Reza Zolfaghari Emameh and others
Database, Volume 2021, 2021, baab029, https://doi.org/10.1093/database/baab029
emiRIT: a text-mining-based resource for microRNA information
Debarati Roychowdhury and others
Database, Volume 2021, 2021, baab031, https://doi.org/10.1093/database/baab031
BENviewer: a gene interaction network visualization server based on graph embedding model
Yunqing Liu and others
Database, Volume 2021, 2021, baab033, https://doi.org/10.1093/database/baab033
dbGENVOC: database of GENomic Variants of Oral Cancer, with special reference to India
Sanchari Pradhan and others
Database, Volume 2021, 2021, baab034, https://doi.org/10.1093/database/baab034
ReMeDy: a platform for integrating and sharing published stem cell research data with a focus on iPSC trials
Kirill Borziak and others
Database, Volume 2021, 2021, baab038, https://doi.org/10.1093/database/baab038
Which methods are the most effective in enabling novice users to participate in ontology creation? A usability study
Limin Zhang and others
Database, Volume 2021, 2021, baab035, https://doi.org/10.1093/database/baab035
MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses
Sebastien A Choteau and others
Database, Volume 2021, 2021, baab032, https://doi.org/10.1093/database/baab032
KMDATA: a curated database of reconstructed individual patient-level data from 153 oncology clinical trials
Geoffrey Fell and others
Database, Volume 2021, 2021, baab037, https://doi.org/10.1093/database/baab037
TIDB: a comprehensive database of trained immunity
Yang Cao and others
Database, Volume 2021, 2021, baab041, https://doi.org/10.1093/database/baab041
CNVIntegrate: the first multi-ethnic database for identifying copy number variations associated with cancer
Amrita Chattopadhyay and others
Database, Volume 2021, 2021, baab044, https://doi.org/10.1093/database/baab044
MUSTARD—a comprehensive resource of mutation-specific therapies in cancer
Gauri Mittal and others
Database, Volume 2021, 2021, baab042, https://doi.org/10.1093/database/baab042
Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students
Paula Duek and others
Database, Volume 2021, 2021, baab046, https://doi.org/10.1093/database/baab046
Male Infertility Knowledgebase: decoding the genetic and disease landscape
Shaini Joseph and Smita D Mahale
Database, Volume 2021, 2021, baab049, https://doi.org/10.1093/database/baab049
The Breeding Information Management System (BIMS): an online resource for crop breeding
Sook Jung and others
Database, Volume 2021, 2021, baab054, https://doi.org/10.1093/database/baab054
MODB: a comprehensive mitochondrial genome database for Mollusca
Jiangyong Qu and others
Database, Volume 2021, 2021, baab056, https://doi.org/10.1093/database/baab056
QSDB—a graphical Quorum Sensing Database
Karsten Klein and others
Database, Volume 2021, 2021, baab058, https://doi.org/10.1093/database/baab058
COVIDium: a COVID-19 resource compendium
Rohit Satyam and others
Database, Volume 2021, 2021, baab057, https://doi.org/10.1093/database/baab057
EpiSurf: metadata-driven search server for analyzing amino acid changes within epitopes of SARS-CoV-2 and other viral species
Anna Bernasconi and others
Database, Volume 2021, 2021, baab059, https://doi.org/10.1093/database/baab059
Classifying domain-specific text documents containing ambiguous keywords
Kamran Karimi and others
Database, Volume 2021, 2021, baab062, https://doi.org/10.1093/database/baab062

Review

The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research
Lauren Chan and others
Database, Volume 2021, 2021, baab003, https://doi.org/10.1093/database/baab003
Post-translational modifications in proteins: resources, tools and prediction methods
Shahin Ramazi and Javad Zahiri
Database, Volume 2021, 2021, baab012, https://doi.org/10.1093/database/baab012
An overview of graph databases and their applications in the biomedical domain
Santiago Timón-Reina and others
Database, Volume 2021, 2021, baab026, https://doi.org/10.1093/database/baab026

Database tool

InSexBase: an annotated genomic resource of sex chromosomes and sex-biased genes in insects
X i Chen and others
Database, Volume 2021, 2021, baab001, https://doi.org/10.1093/database/baab001
bc-GenExMiner 4.5: new mining module computes breast cancer differential gene expression analyses
Pascal Jézéquel and others
Database, Volume 2021, 2021, baab007, https://doi.org/10.1093/database/baab007
CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator
Vasundra Touré and others
Database, Volume 2021, 2021, baaa107, https://doi.org/10.1093/database/baaa107
MENSAdb: a thorough structural analysis of membrane protein dimers
Pedro Matos-Filipe and others
Database, Volume 2021, 2021, baab013, https://doi.org/10.1093/database/baab013
H3ABioNet genomic medicine and microbiome data portals hackathon proceedings
Faisal M Fadlelmola and others
Database, Volume 2021, 2021, baab016, https://doi.org/10.1093/database/baab016
BC-TFdb: a database of transcription factor drivers in breast cancer
Abbas Khan and others
Database, Volume 2021, 2021, baab018, https://doi.org/10.1093/database/baab018
IBDDB: a manually curated and text-mining-enhanced database of genes involved in inflammatory bowel disease
Farhat Khan and others
Database, Volume 2021, 2021, baab022, https://doi.org/10.1093/database/baab022
mPPI: a database extension to visualize structural interactome in a one-to-many manner
Yekai Zhou and others
Database, Volume 2021, 2021, baab036, https://doi.org/10.1093/database/baab036
LINPS: a database for cancer-cell-specific perturbations of biological networks
Mahmoud Ahmed and Deok Ryong Kim
Database, Volume 2021, 2021, baab048, https://doi.org/10.1093/database/baab048

Database update

SinEx DB 2.0 update 2020: database for eukaryotic single-exon coding sequences
R Jorquera and others
Database, Volume 2021, 2021, baab002, https://doi.org/10.1093/database/baab002
An update of KAIKObase, the silkworm genome database
Ching-chia Yang and others
Database, Volume 2021, 2021, baaa099, https://doi.org/10.1093/database/baaa099
Integration of 1:1 orthology maps and updated datasets into Echinobase
Saoirse Foley and others
Database, Volume 2021, 2021, baab030, https://doi.org/10.1093/database/baab030
The Progenetix oncogenomic resource in 2021
Qingyao Huang and others
Database, Volume 2021, 2021, baab043, https://doi.org/10.1093/database/baab043

Technical report

Bioinformatics tools developed to support BioCompute Objects
Janisha A Patel and others
Database, Volume 2021, 2021, baab008, https://doi.org/10.1093/database/baab008
Standardization of assay representation in the Ontology for Biomedical Investigations
Randi Vita and others
Database, Volume 2021, 2021, baab040, https://doi.org/10.1093/database/baab040
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  • Online ISSN 1758-0463
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