Meetings

Recent preprints

• Sep 19, 2026

  DBCLS BioHackathon 2026 report: QPX: Pathway analysis environment for non-model organisms

  We report progress on Quest for Pathways with eXpression (QPX), a pathway analysis environment for non-model organisms, developed during the DBCLS BioHackathon 2026 (BH26). Building on prior BH23/BH25 work, we demonstrated PathLift, a tool that lifts WikiPathways GPML pathways to other species via ortholog mapping, using an Arabidopsis-to-rice mitochondrial complex I example. We also created annotated pathway maps in QPX integrating transcriptome/proteome data for hypoxic stress response, and transcriptome/metabolome data for the non-model organism Symplocarpus renifolius, which lacks an established gene ID system. This clarified data-formatting requirements for linking QPX maps to expression tables and surfaced a string-identifier handling issue in QPX’s backend, reported upstream. Future work includes reproducible ChEBI ID assignment, automated pathway digitization, and compound-centered functional networks from PubChem/PubTator3 data. less than 1 minute read
• Sep 18, 2026

  DBCLS BioHackathon 2026 report: Variant representation in RDF for precision medicine

  For the life science semantic web community, the provision of genomic variants ready for tools and applications is essential to deliver on the promise of precision medicine. As part of the DBCLS BioHackathon 2026, we here report our efforts on how best to provide variant data in RDF for downstream patient-clinical trial matching applications. less than 1 minute read
• Sep 18, 2026

  Building InterMine databases from RDF Portal

  InterMine databases such as HumanMine integrate many biological data sources, but each source needs its own loader, and keeping those loaders current is costly. The public HumanMine has not had a data release since February 2022. RDF Portal, operated by the Database Division for Life Science, now serves many of the same sources as reviewed RDF, and describes each dataset with an rdf-config model. At the DBCLS BioHackathon 2026 we developed rdfc2im, a tool that maps rdf-config models onto the InterMine data model, keeps the mapping as reviewable data with the evidence for every row, uses RDF Config to generate SPARQL queries to acquire data from RDF Portal, and writes the data into a form that InterMine’s standard loader integrates without new code. We used it to build a working demonstration HumanMine from nine sources and a panel of 113 food- and drug-metabolism genes, with NCBI Gene, the Gene Ontology and Reactome loaded in full. The mine supports search, template queries and list analysis. Real loads found problems that static checks did not, most of them related to the way objects from different sources are identified and merged, and to the limits of public SPARQL endpoints. This report describes our proof of concept. We list what remains to be done before rdfc2im can rebuild a full HumanMine from each RDF Portal release. 1 minute read
• Sep 18, 2026

  OSIRIS-MCP: Towards secure conversational access to research information in OSIRIS

  Research information systems contain structured information about researchers, organisational units, projects, publications, and other research activities. However, answering ad hoc questions for reporting, management, or public communication often still requires manual searches, exports, and synthesis. We developed a prototype Model Context Protocol (MCP) connector for OSIRIS, an open-source research information system, during the DBCLS BioHackathon 2026. The connector gives language-model clients read-only access to a deliberately restricted set of typed search and retrieval tools. It combines a compact, evidence-centred data representation with instance-specific metadata discovery, bounded pagination, dedicated API-client permissions, safe error handling, and either OAuth or static API-key authentication. The work also introduced a general API-client registry in OSIRIS, allowing integrations to receive independently revocable credentials and explicitly assigned permissions. A containerised deployment was validated against a local OSIRIS instance containing synthetic data and tested interactively with MCP clients. The prototype demonstrates that conversational access to institutional research information can be implemented without exposing complete database records or making the language model responsible for access control. Evaluation with real institutional data and deployment guidance remain necessary before production use. 1 minute read
• Sep 4, 2026

  AI-Assisted Variant Review Across Asia: Country-Level Expert Panels, Regional Collaboration, and Global Knowledge Sharing

  Genome and exome sequencing have transformed rare disease diagnosis, yet converting large variant sets into evidence-backed interpretations remains labor-intensive and fragmented. Across Asia, population genomic resources and specialist expertise are expanding, but prioritization, expert review, and reuse of reviewed knowledge are often separated across institutions and countries. We argue that the most useful near-term role of artificial intelligence (AI) is not autonomous variant classification, but reducing the friction between distributed evidence and distributed expert judgment. Building on collaborative platform development by participants from institutions in Japan, Singapore, the Philippines, and Thailand, we propose a common workflow connecting variant prioritization and evidence organization, structured expert review, and reviewed-knowledge sharing. AI can support multilingual phenotype structuring, population-aware candidate prioritization, literature and evidence retrieval, and reuse of previous expert-reviewed records, while final evidence assessment remains expert-governed. Country-operated platforms can preserve local governance and population context while exchanging standardized evidence and interpretations across Asia and contributing appropriate records to global knowledge resources. Initial implementations for variant prioritization and an expert review workspace provide a practical foundation for this model. This Perspective outlines where AI can add value, where human judgment must remain decisive, and how a regionally connected expert-panel network could be built. 1 minute read
• Aug 27, 2026

  Enhancing e!DAL-PGP: A Modern Data Submission Platform for Plant Science Research Data

  As part of the BioHackathon Germany 2025, we report here about the progress of Project 8 -Enhancing e!DAL-PGP: A Modern Data Submission Platform for Plant Science Research Dataduring the event.The increasing volume of data generated in plant research underscores the necessity for efficient data management and sharing solutions. The de.NBI Service e!DAL-PGP (Arend et al., 2016, p. Arend2020) serves as a critical research data repository, facilitating the storage, management, and dissemination of plant research data. However, the current implementation faces significant challenges concerning the submission process and the provision of a submission tool for different operating systems, which complicate user interactions and hinder data contribution. A primary issue with the existing e!DAL-PGP service is the cumbersome nature of maintaining and deploying a submission tool across various OS environments. This requirement necessitates extensive effort to build, test, and provide the application for each platform. Consequently, this fragmentation can lead to delays and inconsistencies in the submission process, ultimately hindering researchers from effectively submitting their valuable data to the repository. To address these challenges, this project proposes the development of a unified and user-friendly web submission tool that streamlines the data submission process to eliminate the complexities associated with OS-specific requirements and to ensure that all users can submit their data seamlessly. This simplifies the submission process and enhances usability by focussing onimproving the design and functionality. A well-structured and user-centric form is essential for facilitating accurate and complete data submissions. The current interface lacks features that enhance user experience, such as lookup services, contextual help, and clear instructions. By incorporating these elements, we aim to create a more efficient and engaging submission experience, encouraging researchers to contribute their valuable data without unnecessary complexity. This initiative aligns closely with the goals of de.NBI, which emphasizes the provision of high-quality bioinformatics services and the facilitation of FAIR Research Data Management (RDM). Enhancing the e!DAL-PGP service will streamline the data submission process andpromote a culture of collaboration and data sharing within the plant research community. 1 minute read
• Aug 17, 2026

  BioHackSWAT4HCLS25 report: Towards an interactive mapping experience for data owners

  At the Barcelona SWAT4HCLS 2025 Hackathon, a hacking group familiarized with and worked on improvements for RDFCraft. A tool for a data onboarding tool that helps with mapping tabular or JSON formatted data to a reference schema ontology. less than 1 minute read