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Database Cover Image for Volume 2022
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, Xia Tang, Bo Ye, Songfeng Wu, Keyue Ding
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, 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, Bruce Ford, Julian Starr, Anton Reznicek, Limin Zhang, James A Macklin
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, Anna Sandionigi, Marinella Marzano, Graziano Pesole, Monica Santamaria
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, Shiyong Ma, Xuelu Zhang, Zhaoyu Zhai, Lu Zhou, Haodong Tao, Yachen Wang, Jianbo Pan
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, Riadh Ksouri, Chedly Abdelly, Mohsen Hanana
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, Xuanxuan Yu, Choonhan Youn, Jun Zhou, Feifei Xiao
Database, Volume 2022, 2022, baab086, https://doi.org/10.1093/database/baab086
PlantGF: an analysis and annotation platform for plant gene families
Jiaxuan Li, Shuai Yang, Xiaojie Yang, Hui Wu, Heng Tang, Long Yang
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, Linda Yankie, Eric P Nawrocki, Vasuki Palanigobu, Sergiy Gotvyanskyy, Vincent C Calhoun, Michael Kornbluh, Thomas G Smith, Lydia Fleischmann, Denis Sinyakov, Colleen J Bollin, Ilene Karsch-Mizrachi
Database, Volume 2022, 2022, baac006, https://doi.org/10.1093/database/baac006
ImmuneData: an integrated data discovery system for immunology data repositories
Nan Deng, Canglin Wu, Ashraf Yaseen, Hulin Wu
Database, Volume 2022, 2022, baac003, https://doi.org/10.1093/database/baac003
GNIFdb: a neoantigen intrinsic feature database for glioma
Wendong Li, Ting Sun, Muyang Li, Yufei He, Lin Li, Lu Wang, Haoyu Wang, Jing Li, Hao Wen, Yong Liu, Yifan Chen, Yubo Fan, Beibei Xin, Jing Zhang
Database, Volume 2022, 2022, baac004, https://doi.org/10.1093/database/baac004
PSINDB: the postsynaptic protein–protein interaction database
Zsofia E Kalman, Dániel Dudola, Bálint Mészáros, Zoltán Gáspári, Laszlo Dobson
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, Marija Orlic-Milacic, Karen Rothfels, Joel Weiser, Quang M Trinh, Bijay Jassal, Robin A Haw, Lincoln D Stein
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, Yong-Fei Hu, Yan Zhang, Shu-Yi Wei, Bei-Lei Yang, Ying-Ping Xu, Zhi-Li Rong, Dong Wang, Bin Yang
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, Wenjing Yi, Jin Tao, Xiaoqing Liu, Michael Q Zhang, Guiqian Chen, Qi Dai
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, Shibin Song, Pingzhang Wang
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, Eleni Gentekaki, Kevin D Hyde, Yuan-Pin Xiao, Thatsanee Luangharn, Qing Tian, Yuan-Bing Wang, Saisamorn Lumyong
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, Barbara Gravel, Arnau Dillen, Guillaume Smits, Ann Nowé, Sofia Papadimitriou, Tom Lenaerts
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, 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, Jerven Bolleman, Edouard de Castro, Elisabeth Gasteiger, Parit Bansal, Andrea H Auchincloss, Emmanuel Boutet, Lionel Breuza, Cristina Casals-Casas, Anne Estreicher, Marc Feuermann, Damien Lieberherr, Catherine Rivoire, Ivo Pedruzzi, Nicole Redaschi, Alan Bridge
Database, Volume 2022, 2022, baac026, https://doi.org/10.1093/database/baac026
XePhIR: the zebrafish xenograft phenotype interactive repository
A Groenewoud, G Forn-Cuní, F B Engel, B E Snaar-Jagalska
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, Davide Bozzi, Danilo Porro, Maurizio Casiraghi, Massimo Labra, Antonia Bruno
Database, Volume 2022, 2022, baac033, https://doi.org/10.1093/database/baac033
Translational drug–interaction corpus
Shijun Zhang, Hengyi Wu, Lei Wang, Gongbo Zhang, Luis M Rocha, Hagit Shatkay, Lang Li
Database, Volume 2022, 2022, baac031, https://doi.org/10.1093/database/baac031
A Simple Standard for Sharing Ontological Mappings (SSSOM)
Nicolas Matentzoglu, James P Balhoff, Susan M Bello, Chris Bizon, Matthew Brush, Tiffany J Callahan, Christopher G Chute, William D Duncan, Chris T Evelo, Davera Gabriel, John Graybeal, Alasdair Gray, Benjamin M Gyori, Melissa Haendel, Henriette Harmse, Nomi L Harris, Ian Harrow, Harshad B Hegde, Amelia L Hoyt … Christopher J Mungall
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, 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, Michele Leone, Anna Bernasconi, Mark J Carman
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, A Lain, J Campbell, D R FitzPatrick, T I Simpson
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, Takashi Kiuchi, Susumu Katsuma
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, 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, Mialy DeFelice, Brynn Zalmanek, Jay Hodgson, Caroline Morin, Stockard Simon, Julie A Bletz, James A Eddy, Milen Nikolov, Jineta Banerjee, Kalyan Vinnakota, Marco Marasca, Kevin J Boske, Bruce Hoff, Ljubomir Bradic, YooRi Kim, James R Goss, Robert J Allaway
Database, Volume 2022, 2022, baac045, https://doi.org/10.1093/database/baac045
RegEl corpus: identifying DNA regulatory elements in the scientific literature
Samuele Garda, Freyda Lenihan-Geels, Sebastian Proft, Stefanie Hochmuth, Markus Schülke, Dominik Seelow, Ulf Leser
Database, Volume 2022, 2022, baac043, https://doi.org/10.1093/database/baac043
A transcriptome atlas and interactive analysis platform for autoimmune disease
Zhuoqiao Shen, Minghao Fang, Wujianan Sun, Meifang Tang, Nianping Liu, Lin Zhu, Qian Liu, Bin Li, Ruoming Sun, Yu Shi, Chuang Guo, Jun Lin, Kun Qu
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, Gabriele Macari, Enrico Barbierato, Fabio Polticelli
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, Chen-Feng Lin, Jun-Jie Wu, Yun-Peng Zhao
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, Phuong D Nguyen, Dmitry Korkin, Thanh Thieu
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, Rui Antunes, João F. Silva, João R Almeida, Sérgio Matos
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, Johannes Darms, Katharina Heldt, Denise Ducks, Juliane Fluck
Database, Volume 2022, 2022, baac048, https://doi.org/10.1093/database/baac048
dbBIP: a comprehensive bipolar disorder database for genetic research
Xiaoyan Li, Shunshuai Ma, Wenhui Yan, Yong Wu, Hui Kong, Mingshan Zhang, Xiongjian Luo, Junfeng Xia
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, Giobbe Forni, Matteo Brunetti, Aycan Meral, Alberto Spada, Alessio De Biase, Matteo Montagna
Database, Volume 2022, 2022, baac055, https://doi.org/10.1093/database/baac055
HumanMine: advanced data searching, analysis and cross-species comparison
Rachel Lyne, Adrián Bazaga, Daniela Butano, Sergio Contrino, Joshua Heimbach, Fengyuan Hu, Alexis Kalderimis, Mike Lyne, Kevin Reierskog, Radek Stepan, Julie Sullivan, Archie Wise, Yo Yehudi, Gos Micklem
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, Wen-Chao Yeh, Yu-Wen Chiu, Yung-Chun Chang, Min-Huei Hsu, Yi-Shin Chen, Wen-Lian Hsu
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, Susana Lauw, Ka Lee Ma, Nelson Kei, Ka Leong Ma, Yiu On Wong, Ho Yan Lam, Yee Yung Ting, Tsz Kwan Yau, Wenyan Nong, Dandan Huang, Yichun Xie, Peter Chi Keung Cheung, Hoi Shan Kwan
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, Aurore Comte, Guillaume Martin, Pierrick Perelle, Eric M Weitz, Gaëtan Droc, Mathieu Rouard
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, Po-Ting Lai, Chih-Hsuan Wei, Zhiyong Lu
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, Mayank Musaddi, Nita Parekh
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, Qing Han, Tingting Zhao, Shubo Tian, Xin Sui, Keqiao Li, Wanjing Wang, Jian Wang, Ting Hu, Feng Pan, Yuan Zhang, Jinfeng Zhang
Database, Volume 2022, 2022, baac066, https://doi.org/10.1093/database/baac066
MEDFORD: A human- and machine-readable metadata markup language
Polina Shpilker, John Freeman, Hailey McKelvie, Jill Ashey, Jay-Miguel Fonticella, Hollie Putnam, Jane Greenberg, Lenore Cowen, Alva Couch, Noah M Daniels
Database, Volume 2022, 2022, baac065, https://doi.org/10.1093/database/baac065
SC2sepsis: sepsis single-cell whole gene expression database
Yinjiaozhi Li, Ruoming Tan, Yang Chen, Zhaojun Liu, Erzhen Chen, Tingting Pan, Hongping Qu
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, Chie Motono, Katsuhisa Horimoto, Kazuhiko Fukui
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, Jong Kang Lee, Jen-Chieh Han, Richard Tzong-Han Tsai
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, 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, Louise Deléger, Robert Bossy, Pierre Zweigenbaum, Claire Nédellec
Database, Volume 2022, 2022, baac070, https://doi.org/10.1093/database/baac070
CPMCP: a database of Chinese patent medicine and compound prescription
Chang Sun, Jipeng Huang, Rong Tang, Minglei Li, Haili Yuan, Yuxiang Wang, Jin-Mao Wei, Jian Liu
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, Alexis Allot, Robert Leaman, Rezarta Islamaj, Jingcheng Du, Li Fang, Kai Wang, Shuo Xu, Yuefu Zhang, Parsa Bagherzadeh, Sabine Bergler, Aakash Bhatnagar, Nidhir Bhavsar, Yung-Chun Chang, Sheng-Jie Lin, Wentai Tang, Hongtong Zhang, Ilija Tavchioski, Senja Pollak … Zhiyong Lu
Database, Volume 2022, 2022, baac069, https://doi.org/10.1093/database/baac069
EfGD: the Erianthus fulvus genome database
Zhenfeng Qian, Xuzhen Li, Lilian He, Shujie Gu, Qingqing Shen, Xibing Rao, Rongqiong Zhang, Yining Di, Linyan Xie, Xianhong Wang, Shuying Chen, Yang Dong, Fusheng Li
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, Lu Jin, Guangjue Tang, Zhangxiang Zhao, Yunyan Gu, Dan Yang
Database, Volume 2022, 2022, baac077, https://doi.org/10.1093/database/baac077
AGODB: a comprehensive domain annotation database of argonaute proteins
Bowen Li, Shanshan Yang, Jinjin Long, Xue Chen, Qianyue Zhang, Lin Ning, Bifang He, Heng Chen, Jian Huang
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, Douglas Senalik, Massimo Iorizzo, Shelby Ellison, Allen Van Deynze, Philipp W Simon
Database, Volume 2022, 2022, baac079, https://doi.org/10.1093/database/baac079
COTTONOMICS: a comprehensive cotton multi-omics database
Fan Dai, Jiedan Chen, Ziqian Zhang, Fengjun Liu, Jun Li, Ting Zhao, Yan Hu, Tianzhen Zhang, Lei Fang
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, Balázs Bohár, András Hidas, Tamás Korcsmáros, Balázs Papp, Dávid Fazekas, Eszter Ari
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, Zhenxiao Lu, Haisong Feng, Guojun Chen, Yongmei Wang, Congshan Yang, Zhenyu Yue
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, Evianne Rovers, Matthieu Schapira
Database, Volume 2022, 2022, baac088, https://doi.org/10.1093/database/baac088
BCSCdb: a database of biomarkers of cancer stem cells
Shazia Firdous, Abhirupa Ghosh, Sudipto Saha
Database, Volume 2022, 2022, baac082, https://doi.org/10.1093/database/baac082
Full-text chemical identification with improved generalizability and tagging consistency
Hyunjae Kim, Mujeen Sung, Wonjin Yoon, Sungjoon Park, Jaewoo Kang
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, Lynette Hirschman, Karen E Ross, Rose Oughtred, Martin Krallinger, Kara Dolinski, Mike Tyers, Tonia Korves, Cecilia N Arighi
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, Damien Goutte-Gattat, Shawn Zheng Kai Tan, James P Balhoff, Seth Carbon, Anita R Caron, William D Duncan, Joe E Flack, Melissa Haendel, Nomi L Harris, William R Hogan, Charles Tapley Hoyt, Rebecca C Jackson, HyeongSik Kim, Huseyin Kir, Martin Larralde, Julie A McMurry, James A Overton, Bjoern Peters … David Osumi-Sutherland
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, James F Clarke, Sebastian Polak, Barbara Wiśniowska
Database, Volume 2022, 2022, baac091, https://doi.org/10.1093/database/baac091
KinMod database: a tool for investigating metabolic regulation
Kiandokht Haddadi, Rana Ahmed Barghout, Radhakrishnan Mahadevan
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, Chih-Hsuan Wei, Po-Ting Lai, Qingyu Chen, Rezarta Islamaj, Zhiyong Lu
Database, Volume 2022, 2022, baac090, https://doi.org/10.1093/database/baac090
PharmaKoVariome database for supporting genetic testing
Jungeun Kim, Jae-Pil Choi, Min Sun Kim, Jong Bhak
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, Michael Payne, Lijuan Luo, Sophie Octavia, Mark M Tanaka, Vitali Sintchenko, Ruiting Lan
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, Tingting Chen, Yuchen Mu, Xuan Liang, Kai Xiong, Liqiang Ai, Yunyan Gu, Xingxing Fan, Haihai Liang
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, Dung Truong, Choonhan Youn, Subhashini Sivagnanam, Claire Stirm, Kenneth Yoshimoto, Russell A Poldrack, Amitava Majumdar, Scott Makeig
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, Paulina Glazińska, Marcin Zadworny
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, Mario Sänger, Samuele Garda, Fabio Barth, Christoph Alt, Ulf Leser
Database, Volume 2022, 2022, baac098, https://doi.org/10.1093/database/baac098
Acinetobase: the comprehensive database and repository of Acinetobacter strains
Adam Valcek, James Collier, Alexander Botzki, Charles Van der Henst
Database, Volume 2022, 2022, baac099, https://doi.org/10.1093/database/baac099
PlagueKD: a knowledge graph–based plague knowledge database
Jin Li, Jing Gao, Baiyang Feng, Yi Jing
Database, Volume 2022, 2022, baac100, https://doi.org/10.1093/database/baac100
HCDT: an integrated highly confident drug–target resource
Jiaqi Chen, Zhengxin Chen, Rufei Chen, Dehua Feng, Tianyi Li, Huirui Han, Xiaoman Bi, Zhenzhen Wang, Kongning Li, Yongsheng Li, Xia Li, Limei Wang, Jin Li
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, Robert Leaman, David Cissel, Cathleen Coss, Joseph Denicola, Carol Fisher, Rob Guzman, Preeti Gokal Kochar, Nicholas Miliaras, Zoe Punske, Keiko Sekiya, Dorothy Trinh, Deborah Whitman, Susan Schmidt, Zhiyong Lu
Database, Volume 2022, 2022, baac102, https://doi.org/10.1093/database/baac102
LitCovid ensemble learning for COVID-19 multi-label classification
Jinghang Gu, Emmanuele Chersoni, Xing Wang, Chu-Ren Huang, Longhua Qian, Guodong Zhou
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, Alexandre Mestiashvili, Kurt Lachmann, Richard Kwasnicki, Michael Schroeder
Database, Volume 2022, 2022, baac104, https://doi.org/10.1093/database/baac104
CafeteriaSA corpus: scientific abstracts annotated across different food semantic resources
Gjorgjina Cenikj, Eva Valenčič, Gordana Ispirova, Matevž Ogrinc, Riste Stojanov, Peter Korošec, Ermanno Cavalli, Barbara Koroušić Seljak, Tome Eftimov
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, Gobindo Kumar Paul, Suvro Biswas, Taheruzzaman Kazi, Shafquat Mahbub, Mohasana Akter Mita, Shamima Afrose, Ariful Islam, Sheikh Ahaduzzaman, Md. Robiul Hasan, Mst. Sharmin Sultana Shimu, Maria Meha Promi, Mobasshir Noor Shehab, Ekhtiar Rahman, Khaled Mahmud Sujon, Md. Wasim Alom, Anik Modak, Shahriar Zaman, Md. Salah Uddin … Md. Abu Saleh
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, Murugavel Pavalam, Sowmya Indrakumar, Narayanaswamy Srinivasan, Ramanathan Sowdhamini
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, Xin Wang, Cong Ma, Zhi Zeng, Dong-Kai Pu, Shuo Liu, Candy-S Wu, Shixin Chen, Zixin Deng, Feng-Biao Guo
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, Alexander Junge, Tudor I Oprea, Lars Juhl Jensen
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, Jade Hotchkiss, Victoria Nembaware, Ambroise Wonkam, Nicola Mulder
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, Soumya Nayak, Smit Goswami, Vasundhara Gadiyaram, Oommen K Mathew, Ramanathan Sowdhamini
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, Rohit Mishra, Suhail Ahmad, Supriya Hait, Asim Joshi, Amit Dutt
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, Min Wu, Xuhui Huang, Li Wang, Sophia Zhang, Hui Liu, Jie Zheng
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, Victoria C Blake, Laurel Cooper, Charlene P Wight, Steve Michel, H Busra Cagirici, Gerard R Lazo, Clay L Birkett, David J Waring, Jean-Luc Jannink, Ian Holmes, Amanda J Waters, David P Eickholt, Taner Z Sen
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, Iñaki Cervera-Marzal, Audrey David, Yann Reynaud, Nalin Rastogi
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, Anna Maria Anniciello, Pushpak Pati, Daniel Riccio, Giosuè Scognamiglio, Guillaume Jaume, Giuseppe De Pietro, Maurizio Di Bonito, Antonio Foncubierta, Gerardo Botti, Maria Gabrani, Florinda Feroce, Maria Frucci
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, Olga Pantos, Joanne M Kingsbury, Louise Weaver, Kim M Handley, Gavin Lear
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, Fatima Adel, Mohamed A Rezk, Lina Basiouny, Ahmed A Rezk, Ahmed H Abdel-Razek
Database, Volume 2022, 2022, baac013, https://doi.org/10.1093/database/baac013
hCoronavirusesDB: an integrated bioinformatics resource for human coronaviruses
Iman Almansour, 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, Ruchir Mishra, Colin Berry, Neil Crickmore, Bryony C Bonning
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, Saige Xin, Yanshi Hu, Cong Feng, Ming Chen
Database, Volume 2022, 2022, baac051, https://doi.org/10.1093/database/baac051
Multi-omics molecular biomarkers and database of osteoarthritis
Jianhua Li, Xiaotian Yang, Qinjie Chu, Lingjuan Xie, Yuwen Ding, Xiaoxu Xu, Michael P Timko, Longjiang Fan
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, David Stein, Rayees Rahman, Ravi Iyengar, Avner Schlessinger
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, Evan French, Peter Burdette, Srilakshmi Sagiraju, Thomas Neumann, Tamas S Gal, Bridget T McInnes
Database, Volume 2022, 2022, baac063, https://doi.org/10.1093/database/baac063
ProbResist: a database for drug-resistant probiotic bacteria
Wanying Dou, Hemn Barzan Abdalla, Xu Chen, Changyi Sun, Xuefei Chen, Qiwen Tian, Junyi Wang, Wei Zhou, Wei Chi, Xuan Zhou, Hailv Ye, Chuyun Bi, Xuechen Tian, Yixin Yang, Aloysius Wong
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, Yuyang Dou, Daoliang Xia, Zibo Yin, Yangyang Xiang, Lulu Luo, Yuting Zhang, Jun Wang, Tingming Liang
Database, Volume 2022, 2022, baac075, https://doi.org/10.1093/database/baac075
CATA: a comprehensive chromatin accessibility database for cancer
Jianyuan Zhou, Yanshang Li, Haotian Cao, Min Yang, Lingyu Chu, Taisong Li, Zhengmin Yu, Rui Yu, Bo Qiu, Qiuyu Wang, Xuecang Li, Jianjun Xie
Database, Volume 2022, 2022, baab085, https://doi.org/10.1093/database/baab085
TEx-MST: tissue expression profiles of MANE select transcripts
Kuo-Feng Tung, 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, Yining Hu, David Roy Smith
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, 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, Neda Mohammadi, Abdollah Allahverdi, Elham Khalili, Parviz Abdolmaleki
Database, Volume 2022, 2022, baac011, https://doi.org/10.1093/database/baac011

Meeting report

Conference report: Biocuration 2021 Virtual Conference
Federica Quaglia, Rama Balakrishnan, Susan M Bello, Nicole Vasilevsky
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, Rocio Amorin de Hegedus, Cecilia Arighi, Jill Babor, Alex Bateman, Ian Blaby, Crysten Blaby-Haas, Alan J Bridge, Stephen K Burley, Stacey Cleveland, Lucy J Colwell, Ana Conesa, Christian Dallago, Antoine Danchin, Anita de Waard, Adam Deutschbauer, Raquel Dias, Yousong Ding, Gang Fang … Jin Xu
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, Martin Krallinger, Monica Muñoz, Raul Rodriguez-Esteban, Özlem Uzuner, Lynette Hirschman
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, Julien Van Braekel, Kevin Vanneste, Dieter Deforce, Marie-Alice Fraiture, Nancy H C Roosens
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, Shiyong Ma, Xuelu Zhang, Zhaoyu Zhai, Lu Zhou, Haodong Tao, Yachen Wang, Jianbo Pan
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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