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Database Cover Image for Volume 2024
Volume 2024
2024
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EISSN 1758-0463

Volume 2024, 2024

Original Articles

piOxi database: a web resource of germline and somatic tissue piRNAs identified by chemical oxidation
Kai Wang, Bambarendage P U Perera, Rachel K Morgan, Kimberley Sala-Hamrick, Viviana Geron, Laurie K Svoboda, Christopher Faulk, Dana C Dolinoy, Maureen A Sartor
Database, Volume 2024, 2024, baad096, https://doi.org/10.1093/database/baad096
The African Human Microbiome Portal: a public web portal of curated metagenomic metadata
Anmol Kiran, Mariem Hanachi, Nihad Alsayed, Meriem Fassatoui, Ovokeraye H Oduaran, Imane Allali, Suresh Maslamoney, Ayton Meintjes, Lyndon Zass, Jorge Da Rocha, Rym Kefi, Alia Benkahla, Kais Ghedira, Sumir Panji, Nicola Mulder, Faisal M Fadlelmola, Oussema Souiai
Database, Volume 2024, 2024, baad092, https://doi.org/10.1093/database/baad092
SEPDB: a database of secreted proteins
Ruiqing Wang, Chao Ren, Tian Gao, Hao Li, Xiaochen Bo, Dahai Zhu, Dan Zhang, Hebing Chen, Yong Zhang
Database, Volume 2024, 2024, baae007, https://doi.org/10.1093/database/baae007
Filling knowledge gaps in insect conservation by leveraging genetic data from public archives
Serena Baini, Alessio De Biase
Database, Volume 2024, 2024, baae002, https://doi.org/10.1093/database/baae002
An optimized relational database for querying structural patterns in proteins
Renzo Angles, Mauricio Arenas-Salinas, Roberto García, Ben Ingram
Database, Volume 2024, 2024, baad093, https://doi.org/10.1093/database/baad093
An Inflammatory Bowel Diseases Integrated Resources Portal (IBDIRP)
Nie Kai, Cai Qingsong, Ma Kejia, Luo Weiwei, Wu Xing, Chen Xuejie, Cai Lixia, Deng Minzi, Yang Yuanyuan, Wang Xiaoyan
Database, Volume 2024, 2024, baad097, https://doi.org/10.1093/database/baad097
NanoLAS: a comprehensive nanobody database with data integration, consolidation and application
Shuchang Xiong, Zhengwen Liu, Xin Yi, Kai Liu, Bingding Huang, Xin Wang
Database, Volume 2024, 2024, baae003, https://doi.org/10.1093/database/baae003
AHP DB: a reference database of proteins in the human aqueous humor
Tae Jin Lee, Arnav Goyal, Garrett Jones, Joshua Glass, Vishal Doshi, Kathryn Bollinger, Lane Ulrich, Saleh Ahmed, Sai Karthik Kodeboyina, Amy Estes, Marc Töteberg-Harms, Wenbo Zhi, Shruti Sharma, Ashok Sharma
Database, Volume 2024, 2024, baae001, https://doi.org/10.1093/database/baae001
DAPredict: a database for drug action phenotype prediction
Qingkang Meng, Yiyang Cai, Kun Zhou, Fei Xu, Diwei Huo, Hongbo Xie, Meini Yu, Denan Zhang, Xiujie Chen
Database, Volume 2024, 2024, baad095, https://doi.org/10.1093/database/baad095
FGCD: a database of fungal gene clusters related to secondary metabolism
Fuyuan Zhang, Hongzhe Cao, Helong Si, Jinping Zang, Jingao Dong, Jihong Xing, Kang Zhang
Database, Volume 2024, 2024, baae011, https://doi.org/10.1093/database/baae011
ThermoPCD: a database of molecular dynamics trajectories of antibody–antigen complexes at physiologic and fever-range temperatures
Puneet K Singh, Razvan C Stan
Database, Volume 2024, 2024, baae015, https://doi.org/10.1093/database/baae015
Visualization and exploration of linked data using virtual reality
Alexander J Kellmann, Max Postema, Joris de Keijser, Pjotr Svetachov, Rebecca C Wilson, Esther J van Enckevort, Morris A Swertz
Database, Volume 2024, 2024, baae008, https://doi.org/10.1093/database/baae008
A data browsing application for accessing gene and module-level blood transcriptome profiles of healthy pregnant women from high- and low-resource settings
Darawan Rinchai, Tobias Brummaier, Alexandra A Marr, Tanwir Habib, Mohammed Toufiq, Tomoshigue Kino, François Nosten, Souhaila Al Khodor, Annalisa Terranegra, Rose McGready, Basirudeen Syed Ahamed Kabeer, Damien Chaussabel
Database, Volume 2024, 2024, baae021, https://doi.org/10.1093/database/baae021
CoMentG: comprehensive retrieval of generic relationships between biomedical concepts from the scientific literature
Jorge Novoa, Javier López-Ibáñez, Mónica Chagoyen, Juan A G Ranea, Florencio Pazos
Database, Volume 2024, 2024, baae025, https://doi.org/10.1093/database/baae025
Towards building a trustworthy pipeline integrating Neuroscience Gateway and Open Science Chain
S Sivagnanam, S Yeu, K Lin, S Sakai, F Garzon, K Yoshimoto, K Prantzalos, D P Upadhyaya, A Majumdar, S S Sahoo, W W Lytton
Database, Volume 2024, 2024, baae023, https://doi.org/10.1093/database/baae023
LettuceDB: an integrated multi-omics database for cultivated lettuce
Wenhui Zhou, Tao Yang, Liucui Zeng, Jing Chen, Yayu Wang, Xing Guo, Lijin You, Yiqun Liu, Wensi Du, Fan Yang, Cong Hua, Jia Cai, Theo van Hintum, Huan Liu, Ying Gu, Xiaofeng Wei, Tong Wei
Database, Volume 2024, 2024, baae018, https://doi.org/10.1093/database/baae018
ProNet DB: a proteome-wise database for protein surface property representations and RNA-binding profiles
Junkang Wei, Jin Xiao, Siyuan Chen, Licheng Zong, Xin Gao, Yu Li
Database, Volume 2024, 2024, baae012, https://doi.org/10.1093/database/baae012
FoPGDB: a pangenome database of Fusarium oxysporum, a cross-kingdom fungal pathogen
Tan Meng, Hanqing Jiao, Yi Zhang, Yi Zhou, Shaoying Chen, Xinrui Wang, Bowen Yang, Jie Sun, Xin Geng, Dilay Hazal Ayhan, Li Guo
Database, Volume 2024, 2024, baae017, https://doi.org/10.1093/database/baae017
BioKC: a collaborative platform for curation and annotation of molecular interactions
Carlos Vega, Marek Ostaszewski, Valentin Grouès, Reinhard Schneider, Venkata Satagopam
Database, Volume 2024, 2024, baae013, https://doi.org/10.1093/database/baae013
ESKtides: a comprehensive database and mining method for ESKAPE phage-derived antimicrobial peptides
Hongfang Wu, Rongxian Chen, Xuejian Li, Yue Zhang, Jianwei Zhang, Yanbo Yang, Jun Wan, Yang Zhou, Huanchun Chen, Jinquan Li, Runze Li, Geng Zou
Database, Volume 2024, 2024, baae022, https://doi.org/10.1093/database/baae022
Best practices for the manual curation of intrinsically disordered proteins in DisProt
Federica Quaglia, Anastasia Chasapi, Maria Victoria Nugnes, Maria Cristina Aspromonte, Emanuela Leonardi, Damiano Piovesan, Silvio C E Tosatto
Database, Volume 2024, 2024, baae009, https://doi.org/10.1093/database/baae009
AagingBase: a comprehensive database of anti-aging peptides
Kunjulakshmi R, Ambuj Kumar, Keerthana Vinod Kumar, Avik Sengupta, Kavita Kundal, Simran Sharma, Ankita Pawar, Pithani Sai Krishna, Mohammad Alfatah, Sandipan Ray, Bhavana Tiwari, Rahul Kumar
Database, Volume 2024, 2024, baae016, https://doi.org/10.1093/database/baae016
SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues
Zhiwei Zhou, Jingyi Du, Jianhua Wang, Liangyi Liu, M Gracie Gordon, Chun Jimmie Ye, Joseph E Powell, Mulin Jun Li, Shuquan Rao
Database, Volume 2024, 2024, baae010, https://doi.org/10.1093/database/baae010
An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity
Eléonore Bettacchioli, Laurent Chiche, Damien Chaussabel, Divi Cornec, Noémie Jourde-Chiche, Darawan Rinchai
Database, Volume 2024, 2024, baae045, https://doi.org/10.1093/database/baae045
DUVEL: an active-learning annotated biomedical corpus for the recognition of oligogenic combinations
Charlotte Nachtegael, Jacopo De Stefani, Anthony Cnudde, Tom Lenaerts
Database, Volume 2024, 2024, baae039, https://doi.org/10.1093/database/baae039
MechanoBase: a comprehensive database for the mechanics of tissues and cells
Yanhong Xiong, Shiyu Li, Yuxuan Zhang, Qianqian Chen, Mengtan Xing, Yong Zhang, Qi Wang
Database, Volume 2024, 2024, baae040, https://doi.org/10.1093/database/baae040
PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank
Preeti Choudhary, Zukang Feng, John Berrisford, Henry Chao, Yasuyo Ikegawa, Ezra Peisach, Dennis W Piehl, James Smith, Ahsan Tanweer, Mihaly Varadi, John D Westbrook, Jasmine Y Young, Ardan Patwardhan, Kyle L Morris, Jeffrey C Hoch, Genji Kurisu, Sameer Velankar, Stephen K Burley
Database, Volume 2024, 2024, baae041, https://doi.org/10.1093/database/baae041
MSGD: a manually curated database of genomic, transcriptomic, proteomic and drug information for multiple sclerosis
Tao Wu, Yaopan Hou, Guanghao Xin, Jingyan Niu, Shanshan Peng, Fanfan Xu, Ying Li, Yuling Chen, Yifangfei Yu, Huixue Zhang, Xiaotong Kong, Yuze Cao, Shangwei Ning, Lihua Wang, Junwei Hao
Database, Volume 2024, 2024, baae037, https://doi.org/10.1093/database/baae037
PMBC: a manually curated database for prognostic markers of breast cancer
Jiabei Liu, Yiyi Yu, Mingyue Li, Yixuan Wu, Weijun Chen, Guanru Liu, Lingxian Liu, Jiechun Lin, Chujun Peng, Weijun Sun, Xiaoli Wu, Xin Chen
Database, Volume 2024, 2024, baae033, https://doi.org/10.1093/database/baae033
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes
Marija Orlic-Milacic, Karen Rothfels, Lisa Matthews, Adam Wright, Bijay Jassal, Veronica Shamovsky, Quang Trinh, Marc E Gillespie, Cristoffer Sevilla, Krishna Tiwari, Eliot Ragueneau, Chuqiao Gong, Ralf Stephan, Bruce May, Robin Haw, Joel Weiser, Deidre Beavers, Patrick Conley, Henning Hermjakob … Guanming Wu
Database, Volume 2024, 2024, baae031, https://doi.org/10.1093/database/baae031
cancercelllines.org—a novel resource for genomic variants in cancer cell lines
Rahel Paloots, Michael Baudis
Database, Volume 2024, 2024, baae030, https://doi.org/10.1093/database/baae030
MechanoProDB: a web-based database for exploring the mechanical properties of proteins
Ismahene Mesbah, Bianca Habermann, Felix Rico
Database, Volume 2024, 2024, baae047, https://doi.org/10.1093/database/baae047
DRGKB: a knowledgebase of worldwide diagnosis-related groups’ practices for comparison, evaluation and knowledge-guided application
Shumin Ren, Lin Yang, Jiale Du, Mengqiao He, Bairong Shen
Database, Volume 2024, 2024, baae046, https://doi.org/10.1093/database/baae046
The Immunopeptidomics Ontology (ImPO)
Daniel Faria, Patrícia Eugénio, Marta Contreiras Silva, Laura Balbi, Georges Bedran, Ashwin Adrian Kallor, Susana Nunes, Aleksander Palkowski, Michal Waleron, Javier A Alfaro, Catia Pesquita
Database, Volume 2024, 2024, baae014, https://doi.org/10.1093/database/baae014
EUKARYOME: the rRNA gene reference database for identification of all eukaryotes
Leho Tedersoo, Mahdieh S Hosseyni Moghaddam, Vladimir Mikryukov, Ali Hakimzadeh, Mohammad Bahram, R Henrik Nilsson, Iryna Yatsiuk, Stefan Geisen, Arne Schwelm, Kasia Piwosz, Marko Prous, Sirje Sildever, Dominika Chmolowska, Sonja Rueckert, Pavel Skaloud, Peeter Laas, Marco Tines, Jae-Ho Jung, Ji Hye Choi … Sten Anslan
Database, Volume 2024, 2024, baae043, https://doi.org/10.1093/database/baae043
ISTransbase: an online database for inhibitor and substrate of drug transporters
Jinfu Peng, Jiacai Yi, Guoping Yang, Zhijun Huang, Dongsheng Cao
Database, Volume 2024, 2024, baae053, https://doi.org/10.1093/database/baae053
MyxoPortal: a database of myxobacterial genomic features
Rayapadi G Swetha, Benita S Arakal, Santhosh Rajendran, K Sekar, David E Whitworth, Sudha Ramaiah, Philip E James, Paul G Livingstone, Anand Anbarasu
Database, Volume 2024, 2024, baae056, https://doi.org/10.1093/database/baae056
SpadaHC: a database to improve the classification of variants in hereditary cancer genes in the Spanish population
José M Moreno-Cabrera, Lidia Feliubadaló, Marta Pineda, Patricia Prada-Dacasa, Mireia Ramos-Muntada, Jesús Del Valle, Joan Brunet, Bernat Gel, María Currás-Freixes, Bruna Calsina, Milton E Salazar-Hidalgo, Marta Rodríguez-Balada, Bàrbara Roig, Sara Fernández-Castillejo, Mercedes Durán Domínguez, Mónica Arranz Ledo, Mar Infante Sanz, Adela Castillejo, Estela Dámaso … Conxi Lázaro
Database, Volume 2024, 2024, baae055, https://doi.org/10.1093/database/baae055
DrugRepoBank: a comprehensive database and discovery platform for accelerating drug repositioning
Yixian Huang, Danhong Dong, Wenyang Zhang, Ruiting Wang, Yang-Chi-Dung Lin, Huali Zuo, Hsi-Yuan Huang, Hsien-Da Huang
Database, Volume 2024, 2024, baae051, https://doi.org/10.1093/database/baae051
Towards discovery: an end-to-end system for uncovering novel biomedical relations
Tiago Almeida, Richard A A Jonker, Rui Antunes, João R Almeida, Sérgio Matos
Database, Volume 2024, 2024, baae057, https://doi.org/10.1093/database/baae057
HOFE: an interactive forensic entomological database
Mandie Liu, Yihong Qu, Yifei Luo, Binta J J Jallow, Yuting Ma, Afito Luciano, Jingjing Huang, Jifeng Cai, Fanming Meng
Database, Volume 2024, 2024, baae058, https://doi.org/10.1093/database/baae058
MIAMI-AD (Methylation in Aging and Methylation in AD): an integrative knowledgebase that facilitates explorations of DNA methylation across sex, aging, and Alzheimer’s disease
David Lukacsovich, Deirdre O’Shea, Hanchen Huang, Wei Zhang, Juan Young, X Steven Chen, Sven-Thorsten Dietrich, Brian Kunkle, Eden Martin, Lily Wang
Database, Volume 2024, 2024, baae061, https://doi.org/10.1093/database/baae061
PPCRKB: a risk factor knowledge base of postoperative pulmonary complications
Jianchao Duan, Peiyi Li, Aibin Shao, Xuechao Hao, Ruihao Zhou, Cheng Bi, Xingyun Liu, Weimin Li, Huadong Zhu, Guo Chen, Bairong Shen, Tao Zhu
Database, Volume 2024, 2024, baae054, https://doi.org/10.1093/database/baae054
Data set of fraction unbound values in the in vitro incubations for metabolic studies for better prediction of human clearance
Laura Krumpholz, Aleksandra Klimczyk, Wiktoria Bieniek, Sebastian Polak, Barbara Wiśniowska
Database, Volume 2024, 2024, baae063, https://doi.org/10.1093/database/baae063
Transverse aortic constriction multi-omics analysis uncovers pathophysiological cardiac molecular mechanisms
Enio Gjerga, Matthias Dewenter, Thiago Britto-Borges, Johannes Grosso, Frank Stein, Jessica Eschenbach, Mandy Rettel, Johannes Backs, Christoph Dieterich
Database, Volume 2024, 2024, baae060, https://doi.org/10.1093/database/baae060
Improving biomedical entity linking for complex entity mentions with LLM-based text simplification
Florian Borchert, Ignacio Llorca, Matthieu-P Schapranow
Database, Volume 2024, 2024, baae067, https://doi.org/10.1093/database/baae067
Multi-head CRF classifier for biomedical multi-class named entity recognition on Spanish clinical notes
Richard A A Jonker, Tiago Almeida, Rui Antunes, João R Almeida, Sérgio Matos
Database, Volume 2024, 2024, baae068, https://doi.org/10.1093/database/baae068
Dataset of miRNA–disease relations extracted from textual data using transformer-based neural networks
Sumit Madan, Lisa Kühnel, Holger Fröhlich, Martin Hofmann-Apitius, Juliane Fluck
Database, Volume 2024, 2024, baae066, https://doi.org/10.1093/database/baae066
FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants
Chunhui Xu, Trey Shaw, Sai Akhil Choppararu, Yiwei Lu, Shaik Naveed Farooq, Yongfang Qin, Matt Hudson, Brock Weekley, Michael Fisher, Fei He, Jose Roberto Da Silva Nascimento, Nicholas Wergeles, Trupti Joshi, Philip D Bates, Abraham J Koo, Doug K Allen, Edgar B Cahoon, Jay J Thelen, Dong Xu
Database, Volume 2024, 2024, baae074, https://doi.org/10.1093/database/baae074
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII
Rezarta Islamaj, Po-Ting Lai, Chih-Hsuan Wei, Ling Luo, Tiago Almeida, Richard A. A Jonker, Sofia I. R Conceição, Diana F Sousa, Cong-Phuoc Phan, Jung-Hsien Chiang, Jiru Li, Dinghao Pan, Wilailack Meesawad, Richard Tzong-Han Tsai, M. Janina Sarol, Gibong Hong, Airat Valiev, Elena Tutubalina, Shao-Man Lee … Zhiyong Lu
Database, Volume 2024, 2024, baae069, https://doi.org/10.1093/database/baae069
SoDCoD: a comprehensive database of Cu/Zn superoxide dismutase conformational diversity caused by ALS-linked gene mutations and other perturbations
Riko Tabuchi, Yurika Momozawa, Yuki Hayashi, Hisashi Noma, Hidenori Ichijo, Takao Fujisawa
Database, Volume 2024, 2024, baae064, https://doi.org/10.1093/database/baae064
The biomedical relationship corpus of the BioRED track at the BioCreative VIII challenge and workshop
Rezarta Islamaj, Chih-Hsuan Wei, Po-Ting Lai, Ling Luo, Cathleen Coss, Preeti Gokal Kochar, Nicholas Miliaras, Oleg Rodionov, Keiko Sekiya, Dorothy Trinh, Deborah Whitman, Zhiyong Lu
Database, Volume 2024, 2024, baae071, https://doi.org/10.1093/database/baae071
Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy
Karina Martinez, Jon Agirre, Yukie Akune, Kiyoko F Aoki-Kinoshita, Cecilia Arighi, Kristian B Axelsen, Evan Bolton, Emily Bordeleau, Nathan J Edwards, Elisa Fadda, Ten Feizi, Catherine Hayes, Callum M Ives, Hiren J Joshi, Khakurel Krishna Prasad, Sofia Kossida, Frederique Lisacek, Yan Liu, Thomas Lütteke … Raja Mazumder
Database, Volume 2024, 2024, baae073, https://doi.org/10.1093/database/baae073
ncStem: a comprehensive resource of curated and predicted ncRNAs in cancer stemness
Hui Liu, Nan Zhang, Yijie Jia, Jun Wang, Aokun Ye, Siru Yang, Honghan Zhou, Yingli Lv, Chaohan Xu, Shuyuan Wang
Database, Volume 2024, 2024, baae081, https://doi.org/10.1093/database/baae081
GMMID: genetically modified mice information database
Menglin Xu, Minghui Fang, Qiyang Chen, Wenjun Xiao, Zhixuan Xu, Bao Cai, Zhenyang Zhao, Tao Wang, Zhu Zhu, Yingshan Chen, Yue Zhu, Mingzhou Dai, Tiancheng Jiang, Xinyi Li, Siuwing Chun, Runhua Zhou, Yafei Li, Yueyue Gou, Jingjing He … Xuan Jiang
Database, Volume 2024, 2024, baae078, https://doi.org/10.1093/database/baae078
RiceMetaSys: Drought-miR, a one-stop solution for drought responsive miRNAs-mRNA module in rice
Deepesh Kumar, SureshKumar Venkadesan, Ratna Prabha, Shbana Begam, Bipratip Dutta, Dwijesh C Mishra, K K Chaturvedi, Girish Kumar Jha, Amolkumar U Solanke, Amitha Mithra Sevanthi
Database, Volume 2024, 2024, baae076, https://doi.org/10.1093/database/baae076
Autoinhibited Protein Database: a curated database of autoinhibitory domains and their autoinhibition mechanisms
Daeahn Cho, Hyang-Mi Lee, Ji Ah Kim, Jae Gwang Song, Su-hee Hwang, Bomi Lee, Jinsil Park, Kha Mong Tran, Jiwon Kim, Phuong Ngoc Lam Vo, Jooeun Bae, Teerapat Pimt, Kangseok Lee, Jörg Gsponer, Hyung Wook Kim, Dokyun Na
Database, Volume 2024, 2024, baae085, https://doi.org/10.1093/database/baae085
Transformer-based approach for symptom recognition and multilingual linking
Sylvia Vassileva, Georgi Grazhdanski, Ivan Koychev, Svetla Boytcheva
Database, Volume 2024, 2024, baae090, https://doi.org/10.1093/database/baae090
Integrating deep learning architectures for enhanced biomedical relation extraction: a pipeline approach
M Janina Sarol, Gibong Hong, Evan Guerra, Halil Kilicoglu
Database, Volume 2024, 2024, baae079, https://doi.org/10.1093/database/baae079
Recognition and normalization of multilingual symptom entities using in-domain-adapted BERT models and classification layers
Fernando Gallego, Francisco J Veredas
Database, Volume 2024, 2024, baae087, https://doi.org/10.1093/database/baae087
The Australian Biosecurity Genomic Database: a new resource for high-throughput sequencing analysis based on the National Notifiable Disease List of Terrestrial Animals
Jana Batovska, Natasha D Brohier, Peter T Mee, Fiona E Constable, Brendan C Rodoni, Stacey E Lynch
Database, Volume 2024, 2024, baae084, https://doi.org/10.1093/database/baae084
MACSFeD—a database of mosquito acoustic communication and swarming features
YuMin M Loh, Matthew P Su, Kayla G Haruni, Azusa Kamikouchi
Database, Volume 2024, 2024, baae086, https://doi.org/10.1093/database/baae086
Acupuncture indication knowledge bases: meridian entity recognition and classification based on ACUBERT
TianCheng Xu, Jing Wen, Lei Wang, YueYing Huang, ZiJing Zhu, Qian Zhu, Yi Fang, ChengBiao Yang, YouBing Xia
Database, Volume 2024, 2024, baae083, https://doi.org/10.1093/database/baae083
Landscape of racial and ethnic health disparities in the All of Us Research Program
Vincent Lam, Shivam Sharma, John L Spouge, I. King Jordan, Leonardo Mariño-Ramírez
Database, Volume 2024, 2024, baae082, https://doi.org/10.1093/database/baae082
Automatic extraction of transcriptional regulatory interactions of bacteria from biomedical literature using a BERT-based approach
Alfredo Varela-Vega, Ali-Berenice Posada-Reyes, Carlos-Francisco Méndez-Cruz
Database, Volume 2024, 2024, baae094, https://doi.org/10.1093/database/baae094
CBGDA: a manually curated resource for gene–disease associations based on genome-wide CRISPR
Qingsong Du, Zhiyu Zhang, Wanyi Yang, Xunyu Zhou, Nan Zhou, Chuanfang Wu, Jinku Bao
Database, Volume 2024, 2024, baae077, https://doi.org/10.1093/database/baae077
CuPCA: a web server for pan-cancer association analysis of large-scale cuproptosis-related genes
Yishu Xu, Zhenshu Ma, Yajie Wang, Long Zhang, Jiaming Ye, Yuan Chen, Zhengrong Yuan
Database, Volume 2024, 2024, baae075, https://doi.org/10.1093/database/baae075
RegulaTome: a corpus of typed, directed, and signed relations between biomedical entities in the scientific literature
Katerina Nastou, Farrokh Mehryary, Tomoko Ohta, Jouni Luoma, Sampo Pyysalo, Lars Juhl Jensen
Database, Volume 2024, 2024, baae095, https://doi.org/10.1093/database/baae095
Autophagy3D: a comprehensive autophagy structure database
Neha, Jesu Castin, Saman Fatihi, Deepanshi Gahlot, Akanksha Arun, Lipi Thukral
Database, Volume 2024, 2024, baae088, https://doi.org/10.1093/database/baae088
collectNET: a web server for integrated inference of cell–cell communication network
Yan Pan, Zijing Gao, Xuejian Cui, Zhen Li, Rui Jiang
Database, Volume 2024, 2024, baae098, https://doi.org/10.1093/database/baae098
An analysis of FRE @ BC8 SympTEMIST track: named entity recognition
Ander Martinez, Nuria García-Santa
Database, Volume 2024, 2024, baae101, https://doi.org/10.1093/database/baae101
Influenza sequence validation and annotation using VADR
Vincent C Calhoun, Eneida L Hatcher, Linda Yankie, Eric P Nawrocki
Database, Volume 2024, 2024, baae091, https://doi.org/10.1093/database/baae091
PeptiHub: a curated repository of precisely annotated cancer-related peptides with advanced utilities for peptide exploration and discovery
Sara Zareei, Babak Khorsand, Alireza Dantism, Neda Zareei, Fereshteh Asgharzadeh, Shadi Shams Zahraee, Samane Mashreghi Kashan, Shirin Hekmatirad, Shila Amini, Fatemeh Ghasemi, Maryam Moradnia, Atena Vaghf, Anahid Hemmatpour, Hamdam Hourfar, Soudabeh Niknia, Ali Johari, Fatemeh Salimi, Neda Fariborzi, Zohreh Shojaei … Hossein Shabani
Database, Volume 2024, 2024, baae092, https://doi.org/10.1093/database/baae092
Automated annotation of scientific texts for ML-based keyphrase extraction and validation
Oluwamayowa O Amusat, Harshad Hegde, Christopher J Mungall, Anna Giannakou, Neil P Byers, Dan Gunter, Kjiersten Fagnan, Lavanya Ramakrishnan
Database, Volume 2024, 2024, baae093, https://doi.org/10.1093/database/baae093
CPMKG: a condition-based knowledge graph for precision medicine
Jiaxin Yang, Xinhao Zhuang, Zhenqi Li, Gang Xiong, Ping Xu, Yunchao Ling, Guoqing Zhang
Database, Volume 2024, 2024, baae102, https://doi.org/10.1093/database/baae102
Optimized biomedical entity relation extraction method with data augmentation and classification using GPT-4 and Gemini
Cong-Phuoc Phan, Ben Phan, Jung-Hsien Chiang
Database, Volume 2024, 2024, baae104, https://doi.org/10.1093/database/baae104
RettDb: the Rett syndrome omics database to navigate the Rett syndrome genomic landscape
Nico Cillari, Giuseppe Neri, Nadia Pisanti, Paolo Milazzo, Ugo Borello
Database, Volume 2024, 2024, baae109, https://doi.org/10.1093/database/baae109
SMCVdb: a database of experimental cellular toxicity information for drug candidate molecules
Abhay Deep Pandey, Ghanshyam Sharma, Anshula Sharma, Sudhanshu Vrati, Deepak T Nair
Database, Volume 2024, 2024, baae100, https://doi.org/10.1093/database/baae100
Is metadata of articles about COVID-19 enough for multilabel topic classification task?
Shuo Xu, Yuefu Zhang, Liang Chen, Xin An
Database, Volume 2024, 2024, baae106, https://doi.org/10.1093/database/baae106
SesamumGDB: a comprehensive platform for Sesamum genetics and genomics analysis
Cao Hengchun, Guo Hui, Yang Weifei, Li Guiting, Ju Ming, Duan Yinghui, Tian Qiuzhen, Ma Qin, Feng Xiaoxu, Zhang Zhanyou, Zhang Haiyang, Miao Hongmei
Database, Volume 2024, 2024, baae105, https://doi.org/10.1093/database/baae105
PheNormGPT: a framework for extraction and normalization of key medical findings
Ekin Soysal, Kirk Roberts
Database, Volume 2024, 2024, baae103, https://doi.org/10.1093/database/baae103
The Genomic SSR Millets Database (GSMDB): enhancing genetic resources for sustainable agriculture
Sonu Kumar, Sangeeta Singh, Rakesh Kumar, Dinesh Gupta
Database, Volume 2024, 2024, baae114, https://doi.org/10.1093/database/baae114
Genome-wide identification of SSR markers from coding regions for endangered Argania spinosa L. skeels and construction of SSR database: AsSSRdb
Karim Rabeh, Najoua Mghazli, Fatima Gaboun, Abdelkarim Filali-Maltouf, Laila Sbabou, Bouchra Belkadi
Database, Volume 2024, 2024, baae118, https://doi.org/10.1093/database/baae118
Toward clearer recognition and easier usefulness: development of a cross-lingual atherosclerotic cerebrovascular disease ontology
Hetong Ma, Liu Shen, Jiayang Wang, Shilong Wang, Min Wang, Meng Wang, Zixiao Li, Jiao Li
Database, Volume 2024, 2024, baae117, https://doi.org/10.1093/database/baae117
AthRiboNC: an Arabidopsis database for ncRNAs with coding potential revealed from ribosome profiling
Yi Shen, Liya Liu, Enyan Liu, Sida Li, Yuriy Orlov, Vladimir Ivanisenko, Ming Chen
Database, Volume 2024, 2024, baae123, https://doi.org/10.1093/database/baae123
JTIS: enhancing biomedical document-level relation extraction through joint training with intermediate steps
Jiru Li, Dinghao Pan, Zhihao Yang, Yuanyuan Sun, Hongfei Lin, Jian Wang
Database, Volume 2024, 2024, baae125, https://doi.org/10.1093/database/baae125
AneRBC dataset: a benchmark dataset for computer-aided anemia diagnosis using RBC images
Muhammad Shahzad, Syed Hamad Shirazi, Muhammad Yaqoob, Zakir Khan, Assad Rasheed, Israr Ahmed Sheikh, Asad Hayat, Huiyu Zhou
Database, Volume 2024, 2024, baae120, https://doi.org/10.1093/database/baae120
AbAMPdb: a database of Acinetobacter baumannii specific antimicrobial peptides
Farha Anwer, Ahmad Navid, Fiza Faiz, Uzair Haider, Samavi Nasir, Muhammad Farooq, Maryam Zahra, Anosh Bano, Hafiza Hira Bashir, Madiha Ahmad, Syeda Aleena Abbas, Shah E Room, Muhammad Tariq Saeed, Amjad Ali
Database, Volume 2024, 2024, baae096, https://doi.org/10.1093/database/baae096
StopKB: a comprehensive knowledgebase for nonsense suppression therapies
Nicolas Haas, Julie Dawn Thompson, Jean-Paul Renaud, Kirsley Chennen, Olivier Poch
Database, Volume 2024, 2024, baae108, https://doi.org/10.1093/database/baae108
ELiAH: the atlas of E3 ligases in human tissues for targeted protein degradation with reduced off-target effect
Hyojung Paik, Chunryong Oh, Sajid Hussain, Sangjae Seo, Soon Woo Park, Tae Lyun Ko, Ari Lee
Database, Volume 2024, 2024, baae111, https://doi.org/10.1093/database/baae111

Database tool

ARAapp: filling gaps in the ecological knowledge of spiders using an automated and dynamic approach to analyze systematically collected community data
Alexander Bach, Florian Raub, Hubert Höfer, Richard Ottermanns, Martina Roß-Nickoll
Database, Volume 2024, 2024, baae004, https://doi.org/10.1093/database/baae004
STRIDE-DB: a comprehensive database for exploration of instability and phenotypic relevance of short tandem repeats in the human genome
Bharathram Uppili, Mohammed Faruq
Database, Volume 2024, 2024, baae020, https://doi.org/10.1093/database/baae020
IBDTransDB: a manually curated transcriptomic database for inflammatory bowel disease
Victor Avram, Shweta Yadav, Pranav Sahasrabudhe, Dan Chang, Jing Wang
Database, Volume 2024, 2024, baae026, https://doi.org/10.1093/database/baae026
nhanesA: achieving transparency and reproducibility in NHANES research
Laha Ale, Robert Gentleman, Teresa Filshtein Sonmez, Deepayan Sarkar, Christopher Endres
Database, Volume 2024, 2024, baae028, https://doi.org/10.1093/database/baae028
CancerMHL: the database of integrating key DNA methylation, histone modifications and lncRNAs in cancer
Pengyu Du, Yingli Chen, Qianzhong Li, Zhimin Gai, Hui Bai, Luqiang Zhang, Yuxian Liu, Yanni Cao, Yuanyuan Zhai, Wen Jin
Database, Volume 2024, 2024, baae029, https://doi.org/10.1093/database/baae029
A terpenoids database with the chemical content as a novel agronomic trait
Wenqian Li, Yinliang Chen, Ruofei Yang, Zilong Hu, Shaozhong Wei, Sheng Hu, Xinjun Xiong, Meijuan Wang, Ammar Lubeiny, Xiaohua Li, Minglei Feng, Shuang Dong, Xinlu Xie, Chao Nie, Jingyi Zhang, Yunhao Luo, Yichen Zhou, Ruodi Liu, Jinhai Pan … Xuebo Hu
Database, Volume 2024, 2024, baae027, https://doi.org/10.1093/database/baae027
Collecting and managing in situ banana genetic resources information (Musa spp.) using online resources and citizen science
Christophe Jenny, Valentin Guignon, Felip Manyer I Ballester, Max Ruas, Mathieu Rouard
Database, Volume 2024, 2024, baae036, https://doi.org/10.1093/database/baae036
CoSFISH: a comprehensive reference database of COI and 18S rRNA barcodes for fish
Yuanyuan Wang, Yexin Yang, Yi Liu, Chao Liu, Meng Xu, Miao Fang, Xidong Mu
Database, Volume 2024, 2024, baae038, https://doi.org/10.1093/database/baae038
CardioHotspots: a database of mutational hotspots for cardiac disorders
Alberto García S, Mireia Costa, Alba García-Zarzoso, Oscar Pastor
Database, Volume 2024, 2024, baae034, https://doi.org/10.1093/database/baae034
DIRMC: a database of immunotherapy-related molecular characteristics
Yue Liu, Yuhuan Zhou, Xiumei Hu, Wuri Le-Ge, Haoyan Wang, Tao Jiang, Junyi Li, Yang Hu, Yadong Wang
Database, Volume 2024, 2024, baae032, https://doi.org/10.1093/database/baae032
IPAD-DB: a manually curated database for experimentally verified inhibitors of proteins associated with Alzheimer’s disease
Chong Peng, Xiaofeng Liu, Xiangbo Meng, Congge Chen, Xinming Wu, Lin Bai, Fuping Lu, Fufeng Liu
Database, Volume 2024, 2024, baae048, https://doi.org/10.1093/database/baae048
DMLS: an automated pipeline to extract the Drosophila modular transcription regulators and targets from massive literature articles
Tzu-Hsien Yang, Yu-Huai Yu, Sheng-Hang Wu, Fang-Yuan Chang, Hsiu-Chun Tsai, Ya-Chiao Yang
Database, Volume 2024, 2024, baae049, https://doi.org/10.1093/database/baae049
MDDOmics: multi-omics resource of major depressive disorder
Yichao Zhao, Ju Xiang, Xingyuan Shi, Pengzhen Jia, Yan Zhang, Min Li
Database, Volume 2024, 2024, baae042, https://doi.org/10.1093/database/baae042
ImmRNA: a database of RNAs associated with tumor immunity
Fangfang Shen, Zelian Li, Pengfei Wu, Jinpeng Wang
Database, Volume 2024, 2024, baae052, https://doi.org/10.1093/database/baae052
PANGEN: an online platform for the comparison and creation of diagnostic gene panels
Ofer Isakov, Dina Marek-Yagel, Rotem Greenberg, Michal Naftali, Shay Ben-Shachar
Database, Volume 2024, 2024, baae065, https://doi.org/10.1093/database/baae065
Aerial Wildlife Image Repository for animal monitoring with drones in the age of artificial intelligence
Sathishkumar Samiappan, B. Santhana Krishnan, Damion Dehart, Landon R Jones, Jared A Elmore, Kristine O Evans, Raymond B Iglay
Database, Volume 2024, 2024, baae070, https://doi.org/10.1093/database/baae070
Advancing microbiome research through standardized data and metadata collection: introducing the Microbiome Research Data Toolkit
Lyndon Zass, Lamech M Mwapagha, Adetola F Louis-Jacques, Imane Allali, Julius Mulindwa, Anmol Kiran, Mariem Hanachi, Oussama Souiai, Nicola Mulder, Ovokeraye H Oduaran
Database, Volume 2024, 2024, baae062, https://doi.org/10.1093/database/baae062
The text2term tool to map free-text descriptions of biomedical terms to ontologies
Rafael S Gonçalves, Jason Payne, Amelia Tan, Carmen Benitez, Jamie Haddock, Robert Gentleman
Database, Volume 2024, 2024, baae119, https://doi.org/10.1093/database/baae119
athisomiRDB: A comprehensive database of Arabidopsis isomiRs
A T Vivek, Ajay Arya, Supriya P Swain, Shailesh Kumar
Database, Volume 2024, 2024, baae115, https://doi.org/10.1093/database/baae115
Probe my Pathway (PmP): a portal to explore the chemical coverage of the human Reactome
Haejin Angela Kwak, Lihua Liu, Matthieu Schapira
Database, Volume 2024, 2024, baae116, https://doi.org/10.1093/database/baae116
MiCK: a database of gut microbial genes linked with chemoresistance in cancer patients
Muhammad Shahzaib, Muhammad Muaz, Muhammad Hasnain Zubair, Masood Ur Rehman Kayani
Database, Volume 2024, 2024, baae124, https://doi.org/10.1093/database/baae124
scEccDNAdb: an integrated single-cell eccDNA resource for human and mouse
Wenqing Wang, Xinyu Zhao, Tianyu Ma, Tengwei Zhong, Junnuo Zheng, Zhiyun Guo
Database, Volume 2024, 2024, baae126, https://doi.org/10.1093/database/baae126

Database update

FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research
Feng Shao, Minzhi Zeng, Xiaofei Xu, Huahao Zhang, Zuogang Peng
Database, Volume 2024, 2024, baae044, https://doi.org/10.1093/database/baae044
CO-19 PDB 2.0: A Comprehensive COVID-19 Database with Global Auto-Alerts, Statistical Analysis, and Cancer Correlations
Shahid Ullah, Yingmei Li, Wajeeha Rahman, Farhan Ullah, Muhammad Ijaz, Anees Ullah, Gulzar Ahmad, Hameed Ullah, Tianshun Gao
Database, Volume 2024, 2024, baae072, https://doi.org/10.1093/database/baae072
Peptipedia v2.0: a peptide sequence database and user-friendly web platform. A major update
Gabriel Cabas-Mora, Anamaría Daza, Nicole Soto-García, Valentina Garrido, Diego Alvarez, Marcelo Navarrete, Lindybeth Sarmiento-Varón, Julieta H Sepúlveda Yañez, Mehdi D Davari, Frederic Cadet, Álvaro Olivera-Nappa, Roberto Uribe-Paredes, David Medina-Ortiz
Database, Volume 2024, 2024, baae113, https://doi.org/10.1093/database/baae113
GeniePool 2.0: advancing variant analysis through CHM13-T2T, AlphaMissense, gnomAD V4 integration, and variant co-occurrence queries
Grisha Weintraub, Noam Hadar, Ehud Gudes, Shlomi Dolev, Ohad S Birk
Database, Volume 2024, 2024, baae130, https://doi.org/10.1093/database/baae130

Review

Analysis and review of techniques and tools based on machine learning and deep learning for prediction of lysine malonylation sites in protein sequences
Shahin Ramazi, Seyed Amir Hossein Tabatabaei, Elham Khalili, Amirhossein Golshan Nia, Kiomars Motarjem
Database, Volume 2024, 2024, baad094, https://doi.org/10.1093/database/baad094
Global Globin Network and adopting genomic variant database requirements for thalassemia
Hashim Halim-Fikri, Ninie Nadia Zulkipli, Hafiza Alauddin, Celeste Bento, Carsten W Lederer, Petros Kountouris, Marina Kleanthous, Yetti Hernaningsih, Meow-Keong Thong, Muhammad Hamdi Mahmood, Norafiza Mohd Yasin, Ezalia Esa, Jacques Elion, Domenico Coviello, Raja-Zahratul-Azma Raja-Sabudin, Ghada El-Kamah, John Burn, Narazah Mohd Yusoff, Raj Ramesar, Bin Alwi Zilfalil
Database, Volume 2024, 2024, baae080, https://doi.org/10.1093/database/baae080
The importance of graph databases and graph learning for clinical applications
Daniel Walke, Daniel Micheel, Kay Schallert, Thilo Muth, David Broneske, Gunter Saake, Robert Heyer
Database, Volume 2024, 2024, baad045, https://doi.org/10.1093/database/baad045

Perspective/Opinion

Interactive tools for functional annotation of bacterial genomes
Morgan N Price, Adam P Arkin
Database, Volume 2024, 2024, baae089, https://doi.org/10.1093/database/baae089

Technical Report

The relational modeling of hierarchical data in biodiversity databases
Petr Novotný, Jan Wild
Database, Volume 2024, 2024, baae107, https://doi.org/10.1093/database/baae107

Correction

Correction to: The importance of graph databases and graph learning for clinical applications
Database, Volume 2024, 2024, baae006, https://doi.org/10.1093/database/baae006
Correction to: LeishMANIAdb: a comparative resource for Leishmania proteins
Database, Volume 2024, 2024, baae005, https://doi.org/10.1093/database/baae005
Correction to: Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium
Database, Volume 2024, 2024, baae019, https://doi.org/10.1093/database/baae019
Correction to: ESKtides: a comprehensive database and mining method for ESKAPE phage-derived antimicrobial peptides
Database, Volume 2024, 2024, baae035, https://doi.org/10.1093/database/baae035
Correction to: SEPDB: a database of secreted proteins
Database, Volume 2024, 2024, baae024, https://doi.org/10.1093/database/baae024
Correction to: A Terpenoids Database with the Chemical Content as A Novel Agronomic Trait
Database, Volume 2024, 2024, baae050, https://doi.org/10.1093/database/baae050
Correction to: An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity
Database, Volume 2024, 2024, baae059, https://doi.org/10.1093/database/baae059
Correction to: The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII
Database, Volume 2024, 2024, baae110, https://doi.org/10.1093/database/baae110
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