Database: The Journal of Biological Databases and Curation最新文献

{"title":"ProteoformDB: an integrative database for functional roles of proteoforms.","authors":"Hanwen Luo, Sichao Qiu, Maozu Guo, Beibei Xin, Jun Wang, Guoxian Yu","doi":"10.1093/database/baag005","DOIUrl":"10.1093/database/baag005","url":null,"abstract":"<p><p>Proteoforms translated from alternatively spliced transcripts contribute to the functional repertoire of the cell by performing diverse biological functions, contributing to the functional diversity of genomics and proteomics. However, the lack of existing databases that integrate functional annotations of proteoforms, and analyse the drivers of their functional differences significantly hinders in-depth research into proteoform functions. We introduce ProteoformDB, a new web resource with integrated in-platform analytical capabilities, organizes transcript-level functional annotations of proteoforms across multiple species, and provides services for prediction of proteoform functions and analysis of functional regulatory mechanisms. ProteoformDB develops user-friendly interfaces for information search, visualization, function supplement, differential analysis, and data download services. Particularly, it enables users to investigate the impact of molecular events on the function of proteoforms at multiple levels, including sequences, domains, and post-translational modifications, among others, thereby uncovering the functional differences between protein variants. The current version includes processed data (154.83 GB) for 214 animal and 28 plant species, and will become a valuable and expandable proteoform functional resource for studying genome and transcriptome functions, disease mechanisms, and other related research.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2026 ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12883993/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146141300","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"GdbMTB: a manually curated genomic database of magnetotactic bacteria.","authors":"Runjia Ji, Yongxin Pan, Wei Lin","doi":"10.1093/database/baaf090","DOIUrl":"10.1093/database/baaf090","url":null,"abstract":"<p><p>Magnetotactic bacteria (MTB) are a unique group of microorganisms capable of navigating along geomagnetic field lines through the biomineralization of intracellular magnetic nanocrystals called magnetosomes. While genomic analyses have substantially advanced our understanding of these predominantly uncultured microorganisms, MTB genomic data remain scattered across multiple databases with inconsistent quality profiles and incomplete metadata, limiting comprehensive research efforts. To address these challenges, we developed the Genomic Database of Magnetotactic Bacteria (GdbMTB), the first comprehensive, curated genomic resource dedicated to MTB. The current version of GdbMTB integrates 365 publicly available MTB genomes and their associated metadata. Through a standardized bioinformatics workflow, it provides detailed genome quality assessments, taxonomic classifications, and annotations of magnetosome biomineralization genes, ensuring reliable data for downstream analyses. The curated metadata, encompassing environmental context and publication details, offers crucial research background, enabling users to trace the provenance of each genome. Additionally, GdbMTB offers a suite of bioinformatics tools and an analysis pipeline to facilitate advanced MTB studies. GdbMTB enhances accessibility to MTB genomic data, thereby promoting interdisciplinary research in microbiology, geomicrobiology, and biomineralization studies. Database URL: https://www.gdbmtb.cn/.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2026 ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12805115/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145970396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PaVarDB: a database and web platform for missense variant analysis in Pseudomonas aeruginosa using an end-to-end BVbase pipeline.","authors":"Virudhagiri Elamurugan, Subbiah Thamotharan, Vigneshwar Ramakrishnan","doi":"10.1093/database/baag014","DOIUrl":"10.1093/database/baag014","url":null,"abstract":"<p><p>Genomic variant data are useful in detecting and treating antibiotic-resistant bacteria. However, there are no bacterial genomic variant databases that catalogue the variations in the different genes across strains. In this work a Nextflow- and Docker-based end-to-end pipeline, BVbase, that can automate the creation of databases from raw high-throughput sequences has been created to fill this lacuna with Pseudomonas aeruginosa as a case study. Pseudomonas aeruginosa is a Gram-negative adaptable pathogen with multiple antibiotic resistances that causes various types of infections, including respiratory, urinary, and bloodstream infections. The pipeline can take multistrain genomic files, detect missense variants, and save results in a database with the help of Python and SQLite (https://github.com/bic-sastra/BVbase). Using the generated database for P. aeruginosa, a web application interface has been made using Flask and HTML that runs in a server with MySQL backend (https://bic.sastra.edu/pavardb). The web application provides supports for different types of queries to select variants by gene, geographical group, isolation country, antibiotics, and resistance phenotype. This web interface generates results as variant tables, plots, and statistics for the selected data. By enabling interactive visualizations and advanced selection, the platform supports research and clinical use through the exploration of genomic variations associated with antimicrobial resistance.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2026 ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13010064/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147503356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Epilepsy disease classification: a community effort to enhance the Mondo Disease Ontology.","authors":"Nicole Vasilevsky, Sarah Gehrke, Kathleen Mullen, Subit Barua, Ian Braun, Tobias Brünger, Curtis Coughlin, Alina Ivaniuk, Daniel Korn, Dennis Lal, Stephanie Marsh, Elaine O'Loughlin, Daniel Olson, Yousif Shwetar, Christalena Sofocleous, Vanessa Vogel-Farley, Heidi Grabenstatter, Melissa Haendel, Christopher Mungall, Sabrina Toro","doi":"10.1093/database/baag004","DOIUrl":"10.1093/database/baag004","url":null,"abstract":"<p><strong>Motivation: </strong>Epilepsy is a diverse group of neurological disorders affecting over 50 million people worldwide. While common epilepsy types are well studied, rare epilepsies-often severe and genetically complex-pose significant challenges in diagnosis, research, and treatment. Accurate and interoperable etiology and disease classifications are critical for improving data sharing, supporting clinical decision-making, and advancing rare disease research.</p><p><strong>Results: </strong>To enhance the accuracy of epilepsy-related disease concept representation within the Mondo Disease Ontology (Mondo), we conducted a series of expert-driven workshops in collaboration with the team from the Rare Disease Cures Accelerator-Data and Analytics Platform (RDCA-DAP). Specialists in epileptology, genetics, neurodevelopment, biomedical ontology, and patient community advocates systematically reviewed and revised the epilepsy hierarchy in Mondo, aligning it with the International League Against Epilepsy (ILAE) classification system. These updates include reclassification of epilepsy subtypes, including syndromes, age-related epilepsies, and developmental epileptic encephalopathies, resulting in a more granular, standardized, and clinically relevant structure. Mondo now offers an enhanced framework for integrating epilepsy data across resources, enabling improved interoperability and facilitating rare disease research and data curation, with continued efforts underway to further refine and expand this integration.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2026 ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12908683/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146206868","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"IsoProDB: an integrated map of human protein isoforms for accelerated research.","authors":"Sreelakshmi Pathappillil Soman, Samseera Ummar, Muktar Ahmed, Prathik Basthikoppa Shivamurthy, Sourav Sreelan, Poornima Ramesh, Mahammad Nisar, Yashwanth Subbannayya, Rajesh Raju","doi":"10.1093/database/baag015","DOIUrl":"10.1093/database/baag015","url":null,"abstract":"<p><p>Emerging studies highlight the importance of protein isoforms, which often exhibit distinct functional roles and contribute to physiological diversity, disease mechanisms, and phenotypic variation, despite originating from the same gene. However, comprehensive isoform-level resources that characterize protein isoforms remain limited. IsoProDB is an integrative and unified one-stop database that aligns protein isoforms from RefSeq and UniProtKB, enabling cross-sequence visualization for protein isoform analysis in humans. It integrates features such as domain architecture, intrinsically disordered regions, sequence variants, transmembrane topology, and 52 distinct post-translational modifications (PTMs) mapped to protein isoforms from multiple resources. Currently, IsoProDB enables users to perform gene wise comparative analyses across 110 149 protein isoforms derived from 20 536 protein-coding genes for all integrated features, supported by effective visualizations. This provides insights into conserved and nonconserved PTM sites, domains, isoform-specific membrane localization, the impact of variants on protein function, and disease relevance across protein isoforms. With specific isoforms emerging as markers and theragnostic targets for various disorders, IsoProDB is integrated with multiple global resources for easy navigation and exploration of multiomics information on isoforms.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2026 ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13019292/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147510248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Portuguese Beacon: sharing genomic variant data safely.","authors":"Jorge S Oliveira, Sara Sant'Ana, Miguel Santos, Daniel Faria","doi":"10.1093/database/baag012","DOIUrl":"10.1093/database/baag012","url":null,"abstract":"<p><p>Projects such as the European 1+ Million Genomes initiative and the European Genomic Data Infrastructure project are paving the way towards the age of genomic medicine. To address the challenge of balancing genomic data privacy with biomedical research, the proposed solution is to enable discovery of private datasets through public metadata. Yet enabling data discovery based on genomic variants present in a dataset-which is the goal of Beacon-raises the risk of re-identifying data subjects. We have implemented a Portuguese Beacon endpoint within the scope of the European Genomic Data Infrastructure project, which features a re-identification prevention algorithm to ensure the privacy of data subjects-the first Beacon endpoint to do so. We assessed the impact of the algorithm on data discovery, which varies with the size of the Beacon dataset.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2026 ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12993452/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147472987","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ePerturbDB: enhancer's experimental perturbation database.","authors":"Samiksha Maurya, Jaidev Sharma, Amit Mandoli, Vibhor Kumar","doi":"10.1093/database/baaf084","DOIUrl":"10.1093/database/baaf084","url":null,"abstract":"<p><p>Enhancers act as cis-regulatory elements, controlling the expression of genes according to developmental stages, external signalling, and cell states. Recent studies have shown the impact of perturbation of enhancer activity on expression of genes and cell properties. However, at the same time, perturbation of many enhancers does not always show substantial effect on the expression of genes or properties of cells. Hence, there is a need to identify enhancers that can be effectively targeted for therapeutics and understanding regulation. Therefore, a comprehensive resource containing information on the effect of knockdown of enhancers is needed. Here, we introduce a database ePerturbDB, which provides resources to search the effects of 83 743 experimental perturbations of enhancers. The ePerturbDB database allows users to compare their genomic loci to the list of perturbed enhancers to know their potential effect. It also provides enriched genes and ontology terms for query enhancer location overlapping with a known experimentally perturbed enhancer list. Thus, the resource and tool in ePerturbDB can help users build hypotheses and design experiments to find effective enhancer-based therapeutics and inferences about the regulation of cell states. Database URL: http://reggen.iiitd.edu.in:1207/ePerturbDB-html/.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2026 ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12805113/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145970457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Sickle Africa Data Coordinating Centre (SADaCC): a data science hub for interdisciplinary sickle cell disease research and training.","authors":"Ambroise Wonkam, Nchangwi Syntia Munung, Mario Jonas, Wilson Mupfurirwa, Arthemon Nguweneza, Kevin Esoh, Chandre Oosterwyk-Liu, Zimkita Magangana, Khuthala Mnika, Valentina Ngo Bitoungui, Martha Kamkuemah, Kambe Banda, Nabeelah Samie, Jade Hotchkis, Victoria Nembaware, Andre-Pascal Kengne, Nicola Mulder","doi":"10.1093/database/baag007","DOIUrl":"10.1093/database/baag007","url":null,"abstract":"<p><p>Sickle cell disease (SCD) is one of the most prevalent monogenic disorders worldwide, with the highest burden in Africa, where ~75% of the 7.74 million global cases occur. Scientific progress in understanding its epidemiology, clinical heterogeneity, and treatment outcomes has been constrained by heterogeneous, non-standardized, and non-interoperable datasets that limit data integration and cross-country analyses. To address this, the Sickle Africa Data Coordinating Centre (SADaCC) was established as the data science hub of the SickleInAfrica consortium to support the development and expansion of Pan-African SCD registry. SADaCC now coordinates one of the largest patient-consented SCD datasets globally, with data from over 40 000 persons living with SCD in seven countries (Ghana, Mali, Nigeria, Tanzania, Uganda, Zambia, and Zimbabwe) within the Sickle Pan-African Research Consortium (SPARCo), as well as genomic data from SADaCC satellite sites in Cameroon, South Africa, and Malawi. The registry is built on FAIR-compliant architecture, the Sickle Cell Disease Ontology, and powered by a suite of digital platforms such as REDCap, NextCloud, RStudio, GitHub, Docker, and Jupyter. In partnership with SPARCo, SADaCC is also piloting a biobank that will link biospecimens with data in the registry to advance multi-omics research. Beyond infrastructure, SADaCC leads training and/or research in big data analytics, genomics, bioethics, implementation science, qualitative research, and psychosocial studies. Ethical, legal, and social considerations are embedded across all operations with emphasis on equitable intra-African collaboration and patient involvement in research. Looking ahead, SADaCC will integrate real-time data streams, AI-driven analytics, and multi-omics data to drive big data and genetic medicine research for SCD in Africa.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2026 ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12923167/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146257531","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"TCMToxDB: a comprehensive database for the toxicological analysis of traditional Chinese medicines.","authors":"Yongzheng Zhu, Laihao Fang, Yunbo Miao, Longfei Ma, Rong Sun, Yimin Mao, Wei Guo, Jun Wang, Guoxian Yu","doi":"10.1093/database/baag019","DOIUrl":"10.1093/database/baag019","url":null,"abstract":"<p><p>The safety and modernization of traditional Chinese medicine (TCM) are significant concerns for human beings. Recently, the adverse effects caused by the use of certain TCMs have been frequently reported. Although TCMs may cause toxic reactions, they also play critical roles in treating multiple complex diseases. Therefore, toxicity research is urgently needed for the safe usage of TCMs. However, existing databases for TCMs primarily focus on the pharmacological effects of TCMs, with limited attention to the toxicity. They neither distinguish the toxic effects of formulas, herbs, and ingredients, nor classify and summarize targets for specific toxic manifestations, or assemble evidence from previous studies. We developed TCMToxDB, a comprehensive database that focuses on the toxicity and safe usage of TCMs. TCMToxDB systematically integrates and analyses the research results of toxic TCMs, offering users diverse information acquisition and analysis services. In addition, it assembles five canonical herb-target and ingredient-target interaction prediction algorithms with different advantages, which support the prediction of toxic targets of herbs and ingredients to empower the toxicity research of TCMs and to meet users' personal needs. TCMToxDB is accessible at https://www.sdu-idea.cn/TCMToxDB.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2026 ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13083690/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147688796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"VarStack2-an interactive web tool for somatic variant interpretation in cancer.","authors":"Nitin Sreekumar, Benjamin J Ahn, Shulan Tian, Alper Uzun, Ece D Gamsiz Uzun","doi":"10.1093/database/baag016","DOIUrl":"10.1093/database/baag016","url":null,"abstract":"<p><p>The rapid progress in tumour genome sequencing has created a need for bioinformatics tools to interpret the clinical significance of detected variants. VarStack² integrates information from several publicly available resources, including the Catalogue of Somatic Mutations in Cancer (COSMIC), ClinVar, cBioPortal, UCSC Genome Browser, and ClinicalTrials.gov, CIViC and presents it through a user-friendly interface. VarStack2 simplifies the process of retrieving data, saving users significant time compared to manually navigating each database individually. Users can input a variant by specifying a gene symbol, amino acid change, and coding sequence change, with the option to search tumour-specific studies in cBioPortal alongside their primary query. Results are organized into separate sections and can be exported in CSV format for further analysis. Additionally, VarStack2 offers a smart search feature that suggests variants for the gene of interest based on its database search results. These features make VarStack2 a useful tool for scientists and clinicians by enhancing the variant interpretation process and integrating somatic variant information into workflows. VarStack² is freely available at http://varstack.brown.edu/.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2026 ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13070670/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147671206","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}