{"title":"RUM/FILH: a standardized operational capability model for biodiversity databases.","authors":"Miklós Bán","doi":"10.1093/database/baag044","DOIUrl":"10.1093/database/baag044","url":null,"abstract":"<p><p>The increasing reliance of biodiversity research on large-scale databases has brought significant progress in data accessibility but also new challenges in data comparability, reliability, and interpretability. While global platforms, such as GBIF and iNaturalist standardize and disseminate vast quantities of biodiversity information, they cannot fully meet the needs of users relying on local or thematic data sources. In this paper, we propose a unified service capability model, the RUM/FILH model, that provides a transparent, comparable framework for describing database functionalities and data management quality. The RUM model distinguishes three essential data-related services: Read, Upload, and Modify, while the FILH extension integrates FAIR principles and data history accessibility. This combined system enables both users and database administrators to assess interoperability, metadata quality, and licensing conditions quickly and consistently. We demonstrate the applicability of the RUM/FILH model across biodiversity databases of different scales, including international aggregators and community-based platforms. The proposed capability model enhances trust, transparency, and collaboration across distributed data infrastructures, supporting the development of a more coherent and sustainable global biodiversity informatics network.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2026 ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13410939/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148600044","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}
Folorunsho Bright Omage, Ivan Mazoni, Inácio Henrique Yano, Goran Neshich
{"title":"STING-ExositeDB: An AI-assisted curated database of protein exosites for drug discovery.","authors":"Folorunsho Bright Omage, Ivan Mazoni, Inácio Henrique Yano, Goran Neshich","doi":"10.1093/database/baag031","DOIUrl":"10.1093/database/baag031","url":null,"abstract":"<p><strong>Motivation: </strong>Protein exosites are secondary binding sites that recruit macromolecular partners and control molecular recognition across protein families. Despite their therapeutic potential demonstrated by approved drugs such as bivalirudin, systematic characterization remains limited by fragmented literature and inconsistent reporting. Existing databases lack exosite-specific curation, residue-level contact mapping, and structure-function integration.</p><p><strong>Results: </strong>We present ExositeDB, a curated database of protein exosites built through AI-assisted curation combining large language model extraction with expert validation. Our three-pass pipeline acquires papers from multiple databases, extracts data using GPT-4o with confidence scoring, validates findings against PDB structures, and links all claims to source text. The current release contains 525 expert-validated exosite records spanning 280 unique proteins, each annotated with residue-level positions, partner types, and functional roles. Quality is maintained through multi-tier confidence scoring integrating experimental methodology (35% weight), structural validation (25%), literature consistency (20%), and terminology precision (20%). The database follows FAIR principles through structured metadata, versioned releases, persistent identifiers, and an open REST API. Structural coverage includes 395 unique PDB structures supporting structure-function validation. ExositeDB provides training data for AI-driven exosite prediction, supports rational design of selective modulators, and enables analysis of exosite-mediated regulatory networks.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2026 ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13410941/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148600060","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}
Max Štětina, Aleš Křenek, Guglielmo Tedeschi, Filip Krása, Vojtěch Spiwok, Eva Benešová
{"title":"The Asparaginase Database: a comprehensive resource and classification of l-asparaginases.","authors":"Max Štětina, Aleš Křenek, Guglielmo Tedeschi, Filip Krása, Vojtěch Spiwok, Eva Benešová","doi":"10.1093/database/baag045","DOIUrl":"10.1093/database/baag045","url":null,"abstract":"<p><p>l-Asparaginases have been essential anticancer biopharmaceuticals for nearly half a century, particularly in the treatment of acute lymphoblastic leukaemia. Despite their success, current preparations face challenges, such as strong immunogenicity, reduced stability, and secondary l-glutaminase activity. Systematic discovery and engineering of l-asparaginases with desirable properties are hindered by the limitations of existing l-asparaginase classifications being unable to keep pace with rapid sequence discovery or not reflecting the growing diversity of l-asparaginase characteristics. We present The Asparaginase Database, a resource for curated l-asparaginase sequences, conserved motifs, structures, and experimental data organised by a sequence similarity driven classification into 40 phylogenetic families and 14 clans within previously established l-asparaginase classes. This framework provides a new model for the classification of l-asparaginases based on large-scale molecular phylogeny and could enable researchers to navigate l-asparaginase diversity and identify promising candidates for therapeutic development. Database URL: https://asparaginasedb.com/.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2026 ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13425635/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148629745","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":2.7,"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":"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":2.7,"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":"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":2.7,"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":"ARTS-DB 2.0: an expanded database for target-directed genome mining across bacteria and fungi.","authors":"Turgut Mesut Yılmaz, Semih Erdogmus, Caner Bağcı, Nadine Ziemert","doi":"10.1093/database/baag060","DOIUrl":"10.1093/database/baag060","url":null,"abstract":"<p><p>The increasing prevalence of antimicrobial resistance requires efficient strategies to prioritize biosynthetic gene clusters (BGCs) that may encode bioactive compounds with new modes of action. Target-directed genome mining (TDGM) addresses this challenge by leveraging self-resistance determinants encoded within or adjacent to BGCs to generate target hypotheses and prioritize candidate clusters. ARTS and FunARTS automate TDGM for bacterial and fungal genomes by detecting resistance-associated evolutionary signals, including duplicated essential targets, atypical phylogenetic patterns, and BGC co-localization. The Antibiotic Resistant Target Seeker database (ARTS-DB) was originally developed to enable exploration of precomputed TDGM outputs for bacteria. Here, we present ARTS-DB 2.0, a major update that integrates precomputed ARTS and FunARTS results into a single cross-domain resource. ARTS-DB 2.0 contains TDGM outputs for 42 087 high-quality, non-redundant genomes (35 681 bacteria and 6406 fungi) and incorporates updated BGC annotations generated with antiSMASH 8.0 together with an expanded resistance model repertoire, including the NCBI AMR HMM catalog. The web interface supports flexible query construction and gene-centric exploration, and provides extensive cross-links to external protein, biosynthetic, and pharmacology resources (e.g. UniProt, MIBiG, ChEMBL, and DrugBank). ARTS-DB 2.0 enables rapid, large-scale investigation of resistance-associated biosynthetic patterns across bacteria and fungi, supporting resistance-aware target and BGC prioritization for natural product discovery. Database URL: https://arts-db.cs.uni-tuebingen.de/.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2026 ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13613211/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149036681","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}
Jongmyung Jung, Hyeongsoon Hwang, Yein Park, Minju Song, Jaehoon Yun, Hyeon Hwang, Sanghoon Lee, Jiwoong Sohn, Jaewoo Kang
{"title":"Ensemble multi-retrieval methodologies with reasoning model decision in multi-step biomedical QA.","authors":"Jongmyung Jung, Hyeongsoon Hwang, Yein Park, Minju Song, Jaehoon Yun, Hyeon Hwang, Sanghoon Lee, Jiwoong Sohn, Jaewoo Kang","doi":"10.1093/database/baag061","DOIUrl":"10.1093/database/baag061","url":null,"abstract":"<p><p>Robust and trustworthy biomedical question answering (QA) remains a critical challenge for large language models (LLMs), especially in complex domains such as rare diseases, where information is fragmented across multiple sources. MedHopQA 2025 benchmark introduces 10 000 multi-step reasoning questions curated from Wikipedia, requiring systems to extract, connect, and synthesize biomedical knowledge across interlinked documents. In this work, we present a retrieval-augmented generation (RAG) and decision-making framework that integrates diverse retrieval strategies, including Query2Doc-based, Rationale-based, and Web-augmented retrieval, and employs a dedicated Decision Maker model to select or directly generate the most accurate and well-reasoned answers. Our system not only leverages evidence from both Wikipedia and the web but also explicitly evaluates and compares candidate answers to ensure answer reliability and reasoning transparency. Experiments on the test set demonstrate that our ensemble approach achieves state-of-the-art performance, yielding an Exact Match score of 0.84, and highlighting the importance of hybrid retrieval and robust decision-making in advancing biomedical multi-step QA. Furthermore, comprehensive analyses across retrieval stages reveal that mitigating model self-bias and ensuring a balanced integration of diverse sources are crucial for maximizing overall system performance, which ultimately reaches a score of 0.87.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2026 ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13648003/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149135253","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":"Correction to: neomerDB: a comprehensive database of neomer biomarkers in cancer.","authors":"","doi":"10.1093/database/baag043","DOIUrl":"10.1093/database/baag043","url":null,"abstract":"","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2026 ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13386497/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148535444","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}
Rustam Ruslanovich Taktashov, Nadezhda Yurievna Biziukova, Alexander Viktorovich Dmitriev, Olga Aleksandrovna Tarasova
{"title":"MedHopper: an agentic RAG-LLM system for multi-hop biomedical QA.","authors":"Rustam Ruslanovich Taktashov, Nadezhda Yurievna Biziukova, Alexander Viktorovich Dmitriev, Olga Aleksandrovna Tarasova","doi":"10.1093/database/baag047","DOIUrl":"https://doi.org/10.1093/database/baag047","url":null,"abstract":"<p><p>This multi-hop biomedical QA system combines dense retrieval with a bounded agentic workflow for the MedHopQA (BioCreative IX) task, which requires short, entity-centric answers from a Wikipedia-derived corpus evaluated via exact match with normalization. Our approach replaces prior prompt decomposition with a controlled state machine that routes questions into four strategies (direct, definition, intersection, and multi-hop). The pipeline performs dense retrieval with cross-encoder reranking, executes up to three hops of intermediate entity extraction when needed, and applies answer validation with a bounded query-repair loop. On the MedHopQA test set (N = 1000), MedHopper achieves 0.55 Exact Match (MedHopQA evaluation metric) under official CodaBench evaluation. Ablation confirms capped multi-hop execution, reranking, and query repair as primary contributors; validation modules provide smaller consistent gains. Analysis reveals persistent challenges under exact-match scoring, including answer-type inconsistency (chromosome vs cytoband; yes/no vs symptom) and surface variation across plausible lexicalizations. All experiments were run on a single consumer GPU (RTX 5080) with no API dependencies, producing deterministic outputs at zero marginal cost per query.</p>","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2026 ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13472165/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148763321","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}