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Volume 2022
2022
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EISSN 1758-0463

Volume 2022, 2022

Original Articles

PSL-LCCL: a resource for subcellular protein localization in liver cancer cell line SK_HEP1
Fang Huang and others
Database, Volume 2022, 2022, baab087, https://doi.org/10.1093/database/baab087
Automated extraction of genes associated with antibiotic resistance from the biomedical literature
Andre Brincat and Markus Hofmann
Database, Volume 2022, 2022, baab077, https://doi.org/10.1093/database/baab077
Authors’ attitude toward adopting a new workflow to improve the computability of phenotype publications
Hong Cui and others
Database, Volume 2022, 2022, baac001, https://doi.org/10.1093/database/baac001
MetaCOXI: an integrated collection of metazoan mitochondrial cytochrome oxidase subunit-I DNA sequences
Bachir Balech and others
Database, Volume 2022, 2022, baab084, https://doi.org/10.1093/database/baab084
DDPD 1.0: a manually curated and standardized database of digital properties of approved drugs for drug-likeness evaluation and drug development
Qiang Li and others
Database, Volume 2022, 2022, baab083, https://doi.org/10.1093/database/baab083
Halophytes.tn: an innovative database for Tunisian halophyte plant identification, distribution and characterization
Henda Merchaoui and others
Database, Volume 2022, 2022, baab082, https://doi.org/10.1093/database/baab082
SCANNER: a web platform for annotation, visualization and sharing of single cell RNA-seq data
Guoshuai Cai and others
Database, Volume 2022, 2022, baab086, https://doi.org/10.1093/database/baab086
PlantGF: an analysis and annotation platform for plant gene families
Jiaxuan Li and others
Database, Volume 2022, 2022, baab088, https://doi.org/10.1093/database/baab088
Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank
Beverly A Underwood and others
Database, Volume 2022, 2022, baac006, https://doi.org/10.1093/database/baac006
ImmuneData: an integrated data discovery system for immunology data repositories
Nan Deng and others
Database, Volume 2022, 2022, baac003, https://doi.org/10.1093/database/baac003
GNIFdb: a neoantigen intrinsic feature database for glioma
Wendong Li and others
Database, Volume 2022, 2022, baac004, https://doi.org/10.1093/database/baac004
PSINDB: the postsynaptic protein–protein interaction database
Zsofia E Kalman and others
Database, Volume 2022, 2022, baac007, https://doi.org/10.1093/database/baac007
Evaluating the predictive accuracy of curated biological pathways in a public knowledgebase
Adam J Wright and others
Database, Volume 2022, 2022, baac009, https://doi.org/10.1093/database/baac009
FibROAD: a manually curated resource for multi-omics level evidence integration of fibrosis research
Yu-Zhe Sun and others
Database, Volume 2022, 2022, baac015, https://doi.org/10.1093/database/baac015
HPVMD-C: a disease-based mutation database of human papillomavirus in China
Zhenyu Yang and others
Database, Volume 2022, 2022, baac018, https://doi.org/10.1093/database/baac018
ImmuMethy, a database of DNA methylation plasticity at a single cytosine resolution in human blood and immune cells
Huiying Qi and others
Database, Volume 2022, 2022, baac020, https://doi.org/10.1093/database/baac020
https://invertebratefungi.org/: an expert-curated web-based platform for the identification and classification of invertebrate-associated fungi and fungus-like organisms
De-Ping Wei and others
Database, Volume 2022, 2022, baac021, https://doi.org/10.1093/database/baac021
Scaling up oligogenic diseases research with OLIDA: the Oligogenic Diseases Database
Charlotte Nachtegael and others
Database, Volume 2022, 2022, baac023, https://doi.org/10.1093/database/baac023
PCRMS: a database of predicted cis-regulatory modules and constituent transcription factor binding sites in genomes
Pengyu Ni and Zhengchang Su
Database, Volume 2022, 2022, baac024, https://doi.org/10.1093/database/baac024
SwissBioPics—an interactive library of cell images for the visualization of subcellular location data
Philippe Le Mercier and others
Database, Volume 2022, 2022, baac026, https://doi.org/10.1093/database/baac026
XePhIR: the zebrafish xenograft phenotype interactive repository
A Groenewoud and others
Database, Volume 2022, 2022, baac028, https://doi.org/10.1093/database/baac028
SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata
Giulia Agostinetto and others
Database, Volume 2022, 2022, baac033, https://doi.org/10.1093/database/baac033
Translational drug–interaction corpus
Shijun Zhang and others
Database, Volume 2022, 2022, baac031, https://doi.org/10.1093/database/baac031
A Simple Standard for Sharing Ontological Mappings (SSSOM)
Nicolas Matentzoglu and others
Database, Volume 2022, 2022, baac035, https://doi.org/10.1093/database/baac035
AnthraxKP: a knowledge graph-based, Anthrax Knowledge Portal mined from biomedical literature
Baiyang Feng and Jing Gao
Database, Volume 2022, 2022, baac037, https://doi.org/10.1093/database/baac037
GeMI: interactive interface for transformer-based Genomic Metadata Integration
Giuseppe Serna Garcia and others
Database, Volume 2022, 2022, baac036, https://doi.org/10.1093/database/baac036
Creation and evaluation of full-text literature-derived, feature-weighted disease models of genetically determined developmental disorders
T.M Yates and others
Database, Volume 2022, 2022, baac038, https://doi.org/10.1093/database/baac038
SilkBase: an integrated transcriptomic and genomic database for Bombyx mori and related species
Munetaka Kawamoto and others
Database, Volume 2022, 2022, baac040, https://doi.org/10.1093/database/baac040
AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters
Abhijeet Singh and Anna Schnürer
Database, Volume 2022, 2022, baac041, https://doi.org/10.1093/database/baac041
Centralizing neurofibromatosis experimental tool knowledge with the NF Research Tools Database
Ashley Clayton and others
Database, Volume 2022, 2022, baac045, https://doi.org/10.1093/database/baac045
RegEl corpus: identifying DNA regulatory elements in the scientific literature
Samuele Garda and others
Database, Volume 2022, 2022, baac043, https://doi.org/10.1093/database/baac043
A transcriptome atlas and interactive analysis platform for autoimmune disease
Zhuoqiao Shen and others
Database, Volume 2022, 2022, baac050, https://doi.org/10.1093/database/baac050
FGDB: a comprehensive graph database of ligand fragments from the Protein Data Bank
Daniele Toti and others
Database, Volume 2022, 2022, baac044, https://doi.org/10.1093/database/baac044
GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba
Kai-Jie Gu and others
Database, Volume 2022, 2022, baac046, https://doi.org/10.1093/database/baac046
PHILM2Web: A high-throughput database of macromolecular host–pathogen interactions on the Web
Tuan-Dung Le and others
Database, Volume 2022, 2022, baac042, https://doi.org/10.1093/database/baac042
Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics
Tiago Almeida and others
Database, Volume 2022, 2022, baac047, https://doi.org/10.1093/database/baac047
Continuous development of the semantic search engine preVIEW: from COVID-19 to long COVID
Lisa Langnickel and others
Database, Volume 2022, 2022, baac048, https://doi.org/10.1093/database/baac048
dbBIP: a comprehensive bipolar disorder database for genetic research
Xiaoyan Li and others
Database, Volume 2022, 2022, baac049, https://doi.org/10.1093/database/baac049
Curation of a reference database of COI sequences for insect identification through DNA metabarcoding: COins
Giulia Magoga and others
Database, Volume 2022, 2022, baac055, https://doi.org/10.1093/database/baac055
HumanMine: advanced data searching, analysis and cross-species comparison
Rachel Lyne and others
Database, Volume 2022, 2022, baac054, https://doi.org/10.1093/database/baac054
A BERT-based ensemble learning approach for the BioCreative VII challenges: full-text chemical identification and multi-label classification in PubMed articles
Sheng-Jie Lin and others
Database, Volume 2022, 2022, baac056, https://doi.org/10.1093/database/baac056
ProBioQuest: a database and semantic analysis engine for literature, clinical trials and patents related to probiotics
Po Lam Chan and others
Database, Volume 2022, 2022, baac059, https://doi.org/10.1093/database/baac059
GeMo: a web-based platform for the visualization and curation of genome ancestry mosaics
Marilyne Summo and others
Database, Volume 2022, 2022, baac057, https://doi.org/10.1093/database/baac057
A sequence labeling framework for extracting drug–protein relations from biomedical literature
Ling Luo and others
Database, Volume 2022, 2022, baac058, https://doi.org/10.1093/database/baac058
NetREx: Network-based Rice Expression Analysis Server for abiotic stress conditions
Sanchari Sircar and others
Database, Volume 2022, 2022, baac060, https://doi.org/10.1093/database/baac060
Pre-trained models, data augmentation, and ensemble learning for biomedical information extraction and document classification
Arslan Erdengasileng and others
Database, Volume 2022, 2022, baac066, https://doi.org/10.1093/database/baac066
MEDFORD: A human- and machine-readable metadata markup language
Polina Shpilker and others
Database, Volume 2022, 2022, baac065, https://doi.org/10.1093/database/baac065
SC2sepsis: sepsis single-cell whole gene expression database
Yinjiaozhi Li and others
Database, Volume 2022, 2022, baac061, https://doi.org/10.1093/database/baac061
Phosprof: pathway analysis database of drug response based on phosphorylation activity measurements
Harumi Kagiwada and others
Database, Volume 2022, 2022, baac072, https://doi.org/10.1093/database/baac072
Task reformulation and data-centric approach for Twitter medication name extraction
Yu Zhang and others
Database, Volume 2022, 2022, baac067, https://doi.org/10.1093/database/baac067
TRustDB: A comprehensive bioinformatics resource for understanding the complete Wheat—Stem rust host–pathogen interactome
Raghav Kataria and Rakesh Kaundal
Database, Volume 2022, 2022, baac068, https://doi.org/10.1093/database/baac068
Do syntactic trees enhance Bidirectional Encoder Representations from Transformers (BERT) models for chemical–drug relation extraction?
Anfu Tang and others
Database, Volume 2022, 2022, baac070, https://doi.org/10.1093/database/baac070
CPMCP: a database of Chinese patent medicine and compound prescription
Chang Sun and others
Database, Volume 2022, 2022, baac073, https://doi.org/10.1093/database/baac073
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations
Qingyu Chen and others
Database, Volume 2022, 2022, baac069, https://doi.org/10.1093/database/baac069
EfGD: the Erianthus fulvus genome database
Zhenfeng Qian and others
Database, Volume 2022, 2022, baac076, https://doi.org/10.1093/database/baac076
LiqBioer: a manually curated database of cancer biomarkers in body fluid
Yiding Geng and others
Database, Volume 2022, 2022, baac077, https://doi.org/10.1093/database/baac077
AGODB: a comprehensive domain annotation database of argonaute proteins
Bowen Li and others
Database, Volume 2022, 2022, baac078, https://doi.org/10.1093/database/baac078
CarrotOmics: a genetics and comparative genomics database for carrot (Daucus carota)
William R Rolling and others
Database, Volume 2022, 2022, baac079, https://doi.org/10.1093/database/baac079
COTTONOMICS: a comprehensive cotton multi-omics database
Fan Dai and others
Database, Volume 2022, 2022, baac080, https://doi.org/10.1093/database/baac080
TFLink: an integrated gateway to access transcription factor–target gene interactions for multiple species
Orsolya Liska and others
Database, Volume 2022, 2022, baac083, https://doi.org/10.1093/database/baac083
DGPD: a knowledge database of dense granule proteins of the Apicomplexa
Hang Hu and others
Database, Volume 2022, 2022, baac085, https://doi.org/10.1093/database/baac085
ChemBioPort: an online portal to navigate the structure, function and chemical inhibition of the human proteome
Lihua Liu and others
Database, Volume 2022, 2022, baac088, https://doi.org/10.1093/database/baac088
BCSCdb: a database of biomarkers of cancer stem cells
Shazia Firdous and others
Database, Volume 2022, 2022, baac082, https://doi.org/10.1093/database/baac082
Full-text chemical identification with improved generalizability and tagging consistency
Hyunjae Kim and others
Database, Volume 2022, 2022, baac074, https://doi.org/10.1093/database/baac074
Overview of the COVID-19 text mining tool interactive demonstration track in BioCreative VII
Andrew Chatr-aryamontri and others
Database, Volume 2022, 2022, baac084, https://doi.org/10.1093/database/baac084
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies
Nicolas Matentzoglu and others
Database, Volume 2022, 2022, baac087, https://doi.org/10.1093/database/baac087
An open-access data set of pig skin anatomy and physiology for modelling purposes
Laura Krumpholz and others
Database, Volume 2022, 2022, baac091, https://doi.org/10.1093/database/baac091
KinMod database: a tool for investigating metabolic regulation
Kiandokht Haddadi and others
Database, Volume 2022, 2022, baac081, https://doi.org/10.1093/database/baac081
Assigning species information to corresponding genes by a sequence labeling framework
Ling Luo and others
Database, Volume 2022, 2022, baac090, https://doi.org/10.1093/database/baac090
PharmaKoVariome database for supporting genetic testing
Jungeun Kim and others
Database, Volume 2022, 2022, baac092, https://doi.org/10.1093/database/baac092
MGTdb: a web service and database for studying the global and local genomic epidemiology of bacterial pathogens
Sandeep Kaur and others
Database, Volume 2022, 2022, baac094, https://doi.org/10.1093/database/baac094
FDRdb: a manually curated database of fibrotic disease–associated RNAome and high-throughput datasets
Chengyu Wang and others
Database, Volume 2022, 2022, baac095, https://doi.org/10.1093/database/baac095
NEMAR: an open access data, tools and compute resource operating on neuroelectromagnetic data
Arnaud Delorme and others
Database, Volume 2022, 2022, baac096, https://doi.org/10.1093/database/baac096
OakRootRNADB—a consolidated RNA-seq database for coding and noncoding RNA in roots of pedunculate oak (Quercus robur)
Paulina Kościelniak and others
Database, Volume 2022, 2022, baac097, https://doi.org/10.1093/database/baac097
Chemical–protein relation extraction with ensembles of carefully tuned pretrained language models
Leon Weber and others
Database, Volume 2022, 2022, baac098, https://doi.org/10.1093/database/baac098
Acinetobase: the comprehensive database and repository of Acinetobacter strains
Adam Valcek and others
Database, Volume 2022, 2022, baac099, https://doi.org/10.1093/database/baac099
PlagueKD: a knowledge graph–based plague knowledge database
Jin Li and others
Database, Volume 2022, 2022, baac100, https://doi.org/10.1093/database/baac100
HCDT: an integrated highly confident drug–target resource
Jiaqi Chen and others
Database, Volume 2022, 2022, baac101, https://doi.org/10.1093/database/baac101
NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles
Rezarta Islamaj and others
Database, Volume 2022, 2022, baac102, https://doi.org/10.1093/database/baac102
LitCovid ensemble learning for COVID-19 multi-label classification
Jinghang Gu and others
Database, Volume 2022, 2022, baac103, https://doi.org/10.1093/database/baac103
Emati: a recommender system for biomedical literature based on supervised learning
Özge Kart and others
Database, Volume 2022, 2022, baac104, https://doi.org/10.1093/database/baac104
CafeteriaSA corpus: scientific abstracts annotated across different food semantic resources
Gjorgjina Cenikj and others
Database, Volume 2022, 2022, baac107, https://doi.org/10.1093/database/baac107

Database update

phytochemdb: a platform for virtual screening and computer-aided drug designing
Shafi Mahmud and others
Database, Volume 2022, 2022, baac002, https://doi.org/10.1093/database/baac002
DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins
Neha V Kalmankar and others
Database, Volume 2022, 2022, baac005, https://doi.org/10.1093/database/baac005
Anti-CRISPRdb v2.2: an online repository of anti-CRISPR proteins including information on inhibitory mechanisms, activities and neighbors of curated anti-CRISPR proteins
Chuan Dong and others
Database, Volume 2022, 2022, baac010, https://doi.org/10.1093/database/baac010
Diseases 2.0: a weekly updated database of disease–gene associations from text mining and data integration
Dhouha Grissa and others
Database, Volume 2022, 2022, baac019, https://doi.org/10.1093/database/baac019
The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation
Gaston K Mazandu and others
Database, Volume 2022, 2022, baac014, https://doi.org/10.1093/database/baac014
PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe
Teerna Bhattacharyya and others
Database, Volume 2022, 2022, baac025, https://doi.org/10.1093/database/baac025
TMC-SNPdb 2.0: an ethnic-specific database of Indian germline variants
Sanket Desai and others
Database, Volume 2022, 2022, baac029, https://doi.org/10.1093/database/baac029
SynLethDB 2.0: a web-based knowledge graph database on synthetic lethality for novel anticancer drug discovery
Jie Wang and others
Database, Volume 2022, 2022, baac030, https://doi.org/10.1093/database/baac030
GrainGenes: a data-rich repository for small grains genetics and genomics
Eric Yao and others
Database, Volume 2022, 2022, baac034, https://doi.org/10.1093/database/baac034
SITVITBovis—a publicly available database and mapping tool to get an improved overview of animal and human cases caused by Mycobacterium bovis
David Couvin and others
Database, Volume 2022, 2022, baab081, https://doi.org/10.1093/database/baab081
BRACS: A Dataset for BReAst Carcinoma Subtyping in H&E Histology Images
Nadia Brancati and others
Database, Volume 2022, 2022, baac093, https://doi.org/10.1093/database/baac093

Database tool

PlasticDB: a database of microorganisms and proteins linked to plastic biodegradation
Victor Gambarini and others
Database, Volume 2022, 2022, baac008, https://doi.org/10.1093/database/baac008
MicroRNA childhood cancer catalog (M3Cs): a resource for translational bioinformatics toward health informatics in pediatric cancer
Wafaa M Rashed and others
Database, Volume 2022, 2022, baac013, https://doi.org/10.1093/database/baac013
hCoronavirusesDB: an integrated bioinformatics resource for human coronaviruses
Iman Almansour and Imane Boudellioua
Database, Volume 2022, 2022, baac017, https://doi.org/10.1093/database/baac017
BPPRC database: a web-based tool to access and analyse bacterial pesticidal proteins
Suresh Panneerselvam and others
Database, Volume 2022, 2022, baac022, https://doi.org/10.1093/database/baac022
met v1: expanding on old estimations of biodiversity from eDNA with a new database framework
David C Molik
Database, Volume 2022, 2022, baac032, https://doi.org/10.1093/database/baac032
LBD: a manually curated database of experimentally validated lymphoma biomarkers
Bin Tan and others
Database, Volume 2022, 2022, baac051, https://doi.org/10.1093/database/baac051
Multi-omics molecular biomarkers and database of osteoarthritis
Jianhua Li and others
Database, Volume 2022, 2022, baac052, https://doi.org/10.1093/database/baac052
Structural signatures: a web server for exploring a database of and generating protein structural features from human cell lines and tissues
Nicole Zatorski and others
Database, Volume 2022, 2022, baac053, https://doi.org/10.1093/database/baac053
TopEx: topic exploration of COVID-19 corpora - Results from the BioCreative VII Challenge Track 4
Amy L Olex and others
Database, Volume 2022, 2022, baac063, https://doi.org/10.1093/database/baac063
ProbResist: a database for drug-resistant probiotic bacteria
Wanying Dou and others
Database, Volume 2022, 2022, baac064, https://doi.org/10.1093/database/baac064
SLOAD: a comprehensive database of cancer-specific synthetic lethal interactions for precision cancer therapy via multi-omics analysis
Li Guo and others
Database, Volume 2022, 2022, baac075, https://doi.org/10.1093/database/baac075
CATA: a comprehensive chromatin accessibility database for cancer
Jianyuan Zhou and others
Database, Volume 2022, 2022, baab085, https://doi.org/10.1093/database/baab085
TEx-MST: tissue expression profiles of MANE select transcripts
Kuo-Feng Tung and Wen-chang Lin
Database, Volume 2022, 2022, baac089, https://doi.org/10.1093/database/baac089
HSDatabase—a database of highly similar duplicate genes from plants, animals, and algae
Xi Zhang and others
Database, Volume 2022, 2022, baac086, https://doi.org/10.1093/database/baac086
CaRPE: the Carbon Reduction Potential Evaluation tool for building climate mitigation scenarios on US agricultural lands
Daniel K Manter and Jennifer M Moore
Database, Volume 2022, 2022, baac105, https://doi.org/10.1093/database/baac105

Review Articles

A review on antimicrobial peptides databases and the computational tools
Shahin Ramazi and others
Database, Volume 2022, 2022, baac011, https://doi.org/10.1093/database/baac011

Meeting report

Conference report: Biocuration 2021 Virtual Conference
Federica Quaglia and others
Database, Volume 2022, 2022, baac027, https://doi.org/10.1093/database/baac027
A roadmap for the functional annotation of protein families: a community perspective
Valérie de Crécy-lagard and others
Database, Volume 2022, 2022, baac062, https://doi.org/10.1093/database/baac062

Perspective/Opinion

New reasons for biologists to write with a formal language
Raul Rodriguez-Esteban
Database, Volume 2022, 2022, baac039, https://doi.org/10.1093/database/baac039
Challenges and opportunities for mining adverse drug reactions: perspectives from pharma, regulatory agencies, healthcare providers and consumers
Graciela Gonzalez-Hernandez and others
Database, Volume 2022, 2022, baac071, https://doi.org/10.1093/database/baac071
Reviewing knowledgebase and database grant proposals in the life sciences: the role of innovation
Peter D Karp
Database, Volume 2022, 2022, baac106, https://doi.org/10.1093/database/baac106

Correction

Correction to: FEDA (Food Enzyme Database): a web application gathering information about food enzyme preparations available on the European market
Marie Deckers and others
Database, Volume 2022, 2022, baac012, https://doi.org/10.1093/database/baac012
Correction to: DDPD 1.0: a manually curated and standardized database of digital properties of approved drugs for drug-likeness evaluation and drug development
Qiang Li and others
Database, Volume 2022, 2022, baac016, https://doi.org/10.1093/database/baac016
Correction to: Acinetobase: the comprehensive database and repository of Acinetobacter strains
Database, Volume 2022, 2022, baac111, https://doi.org/10.1093/database/baac111
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