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Database - The Journal of Biological Databases and Curation, Volume 2024
Volume 2024, January 2024
- Kai Wang
, Bambarendage P. U. Perera, Rachel K. Morgan, Kimberley Sala-Hamrick, Viviana Geron, Laurie K. Svoboda, Christopher Faulk
piOxi database: a web resource of germline and somatic tissue piRNAs identified by chemical oxidation. - Anmol M. Kiran, Mariem Hanachi
The African Human Microbiome Portal: a public web portal of curated metagenomic metadata. - Ruiqing Wang, Chao Ren
SEPDB: a database of secreted proteins. - Shahin Ramazi, Seyed Amir Hossein Tabatabaei, Elham Khalili, Amirhossein Golshan Nia, Kiomars Motarjem:
Analysis and review of techniques and tools based on machine learning and deep learning for prediction of lysine malonylation sites in protein sequences. - Daniel Walke
The importance of graph databases and graph learning for clinical applications. - Alexander Bach
ARAapp: filling gaps in the ecological knowledge of spiders using an automated and dynamic approach to analyze systematically collected community data. - Shuchang Xiong, Zhengwen Liu, Xin Yi, Kai Liu, Bingding Huang, Xin Wang
NanoLAS: a comprehensive nanobody database with data integration, consolidation and application. - Nie Kai, Cai Qingsong, Ma Kejia, Luo Weiwei, Xing Wu, Chen Xuejie, Cai Lixia, Deng Minzi, Yuan-Yuan Yang, Wang Xiaoyan:
An Inflammatory Bowel Diseases Integrated Resources Portal (IBDIRP). - Qingkang Meng, Yiyang Cai, Kun Zhou, Fei Xu, Diwei Huo, Hongbo Xie, Meini Yu, Denan Zhang, Xiujie Chen
DAPredict: a database for drug action phenotype prediction. - Correction to: The importance of graph databases and graph learning for clinical applications.
- Correction to: LeishMANIAdb: a comparative resource for Leishmania proteins.
- Tae Jin Lee
AHP DB: a reference database of proteins in the human aqueous humor. - Renzo Angles
An optimized relational database for querying structural patterns in proteins. - Serena Baini, Alessio De Biase:
Filling knowledge gaps in insect conservation by leveraging genetic data from public archives. - Kunjulakshmi R, Ambuj Kumar, Keerthana Vinod Kumar, Avik Sengupta, Kavita Kundal, Simran Sharma, Ankita Pawar, Pithani Sai Krishna, Mohammad Alfatah, Sandipan Ray
AagingBase: a comprehensive database of anti-aging peptides. - Zhiwei Zhou
SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues. - Carlos Vega
BioKC: a collaborative platform for curation and annotation of molecular interactions. - Federica Quaglia
Best practices for the manual curation of intrinsically disordered proteins in DisProt. - Fuyuan Zhang, Hongzhe Cao, Helong Si, Jinping Zang, Jingao Dong
FGCD: a database of fungal gene clusters related to secondary metabolism. - Puneet K. Singh, Razvan C. Stan
ThermoPCD: a database of molecular dynamics trajectories of antibody-antigen complexes at physiologic and fever-range temperatures. - Tan Meng, Hanqing Jiao, Yi Zhang, Yi Zhou, Shaoying Chen, Xinrui Wang, Bowen Yang
FoPGDB: a pangenome database of Fusarium oxysporum, a cross-kingdom fungal pathogen. - Hongfang Wu, Rongxian Chen, Xuejian Li, Yue Zhang, Jianwei Zhang
ESKtides: a comprehensive database and mining method for ESKAPE phage-derived antimicrobial peptides. - Victor Avram
IBDTransDB: a manually curated transcriptomic database for inflammatory bowel disease. - Correction to: SEPDB: a database of secreted proteins.
- Subhashini Sivagnanam
Towards building a trustworthy pipeline integrating Neuroscience Gateway and Open Science Chain. - Correction to: Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium.
- Bharathram Uppili
STRIDE-DB: a comprehensive database for exploration of instability and phenotypic relevance of short tandem repeats in the human genome. - Junkang Wei
ProNet DB: a proteome-wise database for protein surface property representations and RNA-binding profiles. - Darawan Rinchai, Tobias Brummaier, Alexandra A. Marr, Tanwir Habib
A data browsing application for accessing gene and module-level blood transcriptome profiles of healthy pregnant women from high- and low-resource settings. - Pengyu Du, Yingli Chen, Qianzhong Li, Zhimin Gai, Hui Bai, Luqiang Zhang, Yuxian Liu, Yanni Cao, Yuanyuan Zhai, Wen Jin:
CancerMHL: the database of integrating key DNA methylation, histone modifications and lncRNAs in cancer. - Jorge Novoa, Javier López-Ibáñez, Monica Chagoyen
CoMentG: comprehensive retrieval of generic relationships between biomedical concepts from the scientific literature. - Alexander Kellmann
Visualization and exploration of linked data using virtual reality. - Wenhui Zhou, Tao Yang
LettuceDB: an integrated multi-omics database for cultivated lettuce. - Laha Ale
nhanesA: achieving transparency and reproducibility in NHANES research. - Rahel Paloots
cancercelllines.org - a novel resource for genomic variants in cancer cell lines. - Marija Orlic-Milacic
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes. - Jiabei Liu, Yiyi Yu, Mingyue Li, Yixuan Wu, Weijun Chen, Guanru Liu, Lingxian Liu, Jiechun Lin, Chujun Peng, Weijun Sun, Xiaoli Wu, Xin Chen:
PMBC: a manually curated database for prognostic markers of breast cancer. - Alberto García S.
CardioHotspots: a database of mutational hotspots for cardiac disorders. 0 - Correction to: ESKtides: a comprehensive database and mining method for ESKAPE phage-derived antimicrobial peptides.
- Yue Liu
DIRMC: a database of immunotherapy-related molecular characteristics. - Daniel Faria, Patrícia Eugénio
The Immunopeptidomics Ontology (ImPO). - Christophe Jenny
Collecting and managing in situ banana genetic resources information (Musa spp.) using online resources and citizen science. - Feng Shao
FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research. - Shumin Ren, Lin Yang, Jiale Du, Mengqiao He, Bairong Shen
DRGKB: a knowledgebase of worldwide diagnosis-related groups' practices for comparison, evaluation and knowledge-guided application. - Eléonore Bettacchioli
An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity. - 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
MSGD: a manually curated database of genomic, transcriptomic, proteomic and drug information for multiple sclerosis. - Yuanyuan Wang, Yexin Yang, Yi Liu, Chao Liu, Meng Xu, Miao Fang, Xidong Mu
CoSFISH: a comprehensive reference database of COI and 18S rRNA barcodes for fish. - Preeti Choudhary
PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank. - Correction to: A Terpenoids Database with the Chemical Content as A Novel Agronomic Trait.
- Charlotte Nachtegael
DUVEL: an active-learning annotated biomedical corpus for the recognition of oligogenic combinations. - Wenqian Li
A terpenoids database with the chemical content as a novel agronomic trait. - Leho Tedersoo
EUKARYOME: the rRNA gene reference database for identification of all eukaryotes. - Ismahene Mesbah
MechanoProDB: a web-based database for exploring the mechanical properties of proteins. - Tzu-Hsien Yang
DMLS: an automated pipeline to extract the Drosophila modular transcription regulators and targets from massive literature articles. 0 - Yanhong Xiong, Shiyu Li, Yuxuan Zhang, Qianqian Chen, Mengtan Xing, Yong Zhang
MechanoBase: a comprehensive database for the mechanics of tissues and cells. - Chong Peng
IPAD-DB: a manually curated database for experimentally verified inhibitors of proteins associated with Alzheimer's disease. - Correction to: An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity.
- Rayapadi G. Swetha, Benita S. Arakal, Santhosh Rajendran, Kanagaraj Sekar, David E. Whitworth, Sudha Ramaiah, Philip E. James
MyxoPortal: a database of myxobacterial genomic features. - Mandie Liu
HOFE: an interactive forensic entomological database. - Fangfang Shen, Zelian Li, Pengfei Wu, Jinpeng Wang:
ImmRNA: a database of RNAs associated with tumor immunity. - Yichao Zhao
MDDOmics: multi-omics resource of major depressive disorder. - Jianchao Duan
PPCRKB: a risk factor knowledge base of postoperative pulmonary complications. - David Lukacsovich, Deirdre O'shea, Hanchen Huang, Wei Zhang, Juan Young, X. Steven Chen, Sven-Thorsten Dietrich, Brian Kunkle, Eden Martin, Lily Wang
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. - Yixian Huang
DrugRepoBank: a comprehensive database and discovery platform for accelerating drug repositioning. - Tiago Melo Almeida
Towards discovery: an end-to-end system for uncovering novel biomedical relations. - Jinfu Peng
ISTransbase: an online database for inhibitor and substrate of drug transporters. - José Marcos Moreno-Cabrera
SpadaHC: a database to improve the classification of variants in hereditary cancer genes in the Spanish population. - Chunhui Xu
FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants. - Sathishkumar Samiappan
Aerial Wildlife Image Repository for animal monitoring with drones in the age of artificial intelligence. - Rezarta Islamaj
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII. - Karina Martinez
Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy. - 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, Lin Luo, Linlin You, Xuan Jiang
GMMID: genetically modified mice information database. - Shahid Ullah
CO-19 PDB 2.0: A Comprehensive COVID-19 Database with Global Auto-Alerts, Statistical Analysis, and Cancer Correlations. - Richard A. A. Jonker
Multi-head CRF classifier for biomedical multi-class named entity recognition on Spanish clinical notes. - Laura Krumpholz
Data set of fraction unbound values in the in vitro incubations for metabolic studies for better prediction of human clearance. - Florian Borchert
Improving biomedical entity linking for complex entity mentions with LLM-based text simplification. - Enio Gjerga, Matthias Dewenter
Transverse aortic constriction multi-omics analysis uncovers pathophysiological cardiac molecular mechanisms. - Ofer Isakov, Dina Marek-Yagel, Rotem Greenberg
PANGEN: an online platform for the comparison and creation of diagnostic gene panels. - Deepesh Kumar, Sureshkumar Venkadesan
RiceMetaSys: Drought-miR, a one-stop solution for drought responsive miRNAs-mRNA module in rice. - Lyndon Zass, Lamech M. Mwapagha, Adetola F. Louis-Jacques, Imane Allali, Julius Mulindwa, Anmol M. Kiran, Mariem Hanachi
Advancing microbiome research through standardized data and metadata collection: introducing the Microbiome Research Data Toolkit. - Riko Tabuchi, Yurika Momozawa, Yuki Hayashi
SoDCoD: a comprehensive database of Cu/Zn superoxide dismutase conformational diversity caused by ALS-linked gene mutations and other perturbations. 0 - Rezarta Islamaj
The biomedical relationship corpus of the BioRED track at the BioCreative VIII challenge and workshop. - Sumit Madan
Dataset of miRNA-disease relations extracted from textual data using transformer-based neural networks. - Hui Liu, Nan Zhang, Yijie Jia, Jun Wang, Aokun Ye, Siru Yang, Honghan Zhou, Yingli Lv, Chaohan Xu
ncStem: a comprehensive resource of curated and predicted ncRNAs in cancer stemness. - Alfredo Varela-Vega
Automatic extraction of transcriptional regulatory interactions of bacteria from biomedical literature using a BERT-based approach. - Qingsong Du
CBGDA: a manually curated resource for gene-disease associations based on genome-wide CRISPR. - Jana Batovska
The Australian Biosecurity Genomic Database: a new resource for high-throughput sequencing analysis based on the National Notifiable Disease List of Terrestrial Animals. - Neha, Jesu Castin, Saman Fatihi, Deepanshi Gahlot, Akanksha Arun, Lipi Thukral
Autophagy3D: a comprehensive autophagy structure database. - Vincent C. Calhoun, Eneida L. Hatcher, Linda Yankie, Eric P. Nawrocki
Influenza sequence validation and annotation using VADR. - Katerina C. Nastou
RegulaTome: a corpus of typed, directed, and signed relations between biomedical entities in the scientific literature. - Fernando Gallego Donoso
Recognition and normalization of multilingual symptom entities using in-domain-adapted BERT models and classification layers. - Hashim Halim-Fikri, Ninie Nadia Zulkipli
Global Globin Network and adopting genomic variant database requirements for thalassemia. - Morgan N. Price
Interactive tools for functional annotation of bacterial genomes. - Sara Zareei, Babak Khorsand
PeptiHub: a curated repository of precisely annotated cancer-related peptides with advanced utilities for peptide exploration and discovery. - Yan Pan
collectNET: a web server for integrated inference of cell-cell communication network. - Yishu Xu, Zhenshu Ma, Yajie Wang, Long Zhang, Jiaming Ye, Yuan Chen
CuPCA: a web server for pan-cancer association analysis of large-scale cuproptosis-related genes. - Yumin M. Loh, Matthew P. Su
MACSFeD - a database of mosquito acoustic communication and swarming features. - M. Janina Sarol
Integrating deep learning architectures for enhanced biomedical relation extraction: a pipeline approach. - Vincent Lam, Shivam Sharma, John L. Spouge
Landscape of racial and ethnic health disparities in the All of Us Research Program. - Tiancheng Xu
Acupuncture indication knowledge bases: meridian entity recognition and classification based on ACUBERT. - Sylvia Vassileva
Transformer-based approach for symptom recognition and multilingual linking. - Daeahn Cho
Autoinhibited Protein Database: a curated database of autoinhibitory domains and their autoinhibition mechanisms. - Ander Martinez, Nuria García-Santa:
An analysis of FRE @ BC8 SympTEMIST track: named entity recognition. - Shuo Xu
Is metadata of articles about COVID-19 enough for multilabel topic classification task? - Abhay Deep Pandey, Ghanshyam Sharma, Anshula Sharma, Sudhanshu Vrati, Deepak T. Nair
SMCVdb: a database of experimental cellular toxicity information for drug candidate molecules. - Oluwamayowa O. Amusat
Automated annotation of scientific texts for ML-based keyphrase extraction and validation. - Hyojung Paik
ELiAH: the atlas of E3 ligases in human tissues for targeted protein degradation with reduced off-target effect. - Ekin Soysal
PheNormGPT: a framework for extraction and normalization of key medical findings. - Cao Hengchun
SesamumGDB: a comprehensive platform for Sesamum genetics and genomics analysis. - Farha Anwer
AbAMPdb: a database of Acinetobacter baumannii specific antimicrobial peptides. - Cong-Phuoc Phan
Optimized biomedical entity relation extraction method with data augmentation and classification using GPT-4 and Gemini. - Nico Cillari, Giuseppe Neri, Nadia Pisanti, Paolo Milazzo, Ugo Borello
RettDb: the Rett syndrome omics database to navigate the Rett syndrome genomic landscape. - Correction to: The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII.
- Jiaxin Yang, Xinhao Zhuang, Zhenqi Li, Gang Xiong, Ping Xu, Yunchao Ling, Guoqing Zhang
CPMKG: a condition-based knowledge graph for precision medicine. - Nicolas Haas, Julie Dawn Thompson, Jean-Paul Renaud, Kirsley Chennen, Olivier Poch
StopKB: a comprehensive knowledgebase for nonsense suppression therapies. - Petr Novotný
The relational modeling of hierarchical data in biodiversity databases. - A. T. Vivek
athisomiRDB: A comprehensive database of Arabidopsis isomiRs. - Gabriel Cabas-Mora
Peptipedia v2.0: a peptide sequence database and user-friendly web platform. A major update. - Sonu Kumar
The Genomic SSR Millets Database (GSMDB): enhancing genetic resources for sustainable agriculture. - Karim Rabeh
Genome-wide identification of SSR markers from coding regions for endangered Argania spinosa L. skeels and construction of SSR database: AsSSRdb. - Rafael S. Gonçalves
The text2term tool to map free-text descriptions of biomedical terms to ontologies. - Jiru Li, Dinghao Pan, Zhihao Yang, Yuanyuan Sun, Hongfei Lin, Jian Wang:
JTIS: enhancing biomedical document-level relation extraction through joint training with intermediate steps. - Muhammad Shahzad, Syed Hamad Shirazi, Muhammad Yaqoob, Zakir Khan, Assad Rasheed, Israr Ahmed Sheikh, Asad Hayat, Huiyu Zhou:
AneRBC dataset: a benchmark dataset for computer-aided anemia diagnosis using RBC images. - Wenqing Wang, Xinyu Zhao, Tianyu Ma, Tengwei Zhong, Junnuo Zheng, Zhiyun Guo:
scEccDNAdb: an integrated single-cell eccDNA resource for human and mouse. - Muhammad Shahzaib, Muhammad Muaz, Muhammad Hasnain Zubair, Masood ur Rehman Kayani:
MiCK: a database of gut microbial genes linked with chemoresistance in cancer patients. - Haejin Angela Kwak, Lihua Liu, Matthieu Schapira:
Probe my Pathway (PmP): a portal to explore the chemical coverage of the human Reactome. - Yi Shen, Liya Liu, Enyan Liu, Sida Li, Yuriy Orlov, Vladimir Ivanisenko, Ming Chen:
AthRiboNC: an Arabidopsis database for ncRNAs with coding potential revealed from ribosome profiling. - Hetong Ma, Liu Shen, Jiayang Wang, Shilong Wang, Min Wang, Meng Wang, Zixiao Li, Jiao Li:
Toward clearer recognition and easier usefulness: development of a cross-lingual atherosclerotic cerebrovascular disease ontology. - Grisha Weintraub, Noam Hadar, Ehud Gudes, Shlomi Dolev, Ohad S. Birk:
GeniePool 2.0: advancing variant analysis through CHM13-T2T, AlphaMissense, gnomAD V4 integration, and variant co-occurrence queries.
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