Meetings

Recent preprints

• Jan 6, 2026

  QPX: Pathway analysis environment

  Building on our work at DBCLS BioHackathon 2023 (BH23), where we introduced QPX and promoted pathway modeling with WikiPathways (Pico et al., 2008) using PathVisio (Kutmon et al., 2015), we now focused on creating new pathway diagrams for diverse species and registering them in WikiPathways with functional annotations. In parallel, we deployed WikiPathways node data into Elasticsearch to enable fast and flexible search and integration of pathway information. less than 1 minute read
• Dec 31, 2025

  BioHackEU25 Report Project 16: MiCoReCa (Microbiome Community Resource Catalogue) - Towards Centralized Curation And Integration Of Microbiome Bioinformatics Resources

  The rapid growth of microbiome research has led to the development of numerous bioinformatics tools and databases, but information about them remains fragmented across disparate, often outdated cataloging efforts, hindering resource discovery and utilization. To address this critical gap, the ELIXIR Microbiome Community proposes the development of MiCoReCa (Microbiome Community Resource Catalogue), a comprehensive, dynamic, open-access catalogue of microbiome-related bioinformatics resources (tools, workflows, training, standards, and databases). Leveraging our community’s expertise, this initiative will utilize standardized ontologies like EDAM and cross-reference established platforms like bio.tools and WorkflowHub to create a centralized, findable inventory. A key feature is the community-driven process for identifying and curating missing ontological terms and metadata, ensuring MiCoReCa’s accuracy and relevance in collaboration with partner platforms. Furthermore, the catalogue will integrate links to training materials from TeSS to support appropriate tool usage, and connect with OpenEBench for benchmarking capabilities. This project will not only provide a vital resource for the microbiome field, enhancing research efficiency and reproducibility, but will also establish a sustainable, adaptable infrastructure potentially applicable to other ELIXIR Communities. This effort represents a significant contribution by the ELIXIR Microbiome Community to streamline microbiome bioinformatics. 1 minute read
• Dec 23, 2025

  Enhancement of the Interoperability of Trait Data on Genetic Resources between Japan and France

  Japan’s National Agriculture and Food Research Organization initiated a collaborative research project with France’s National Research Institute for Agriculture, Food and Environment to evaluate wheat genetic resources and to identify materials with desirable traits using standardized criteria. This paper presents the current status of trait data standardization between the two organizations and outlines a direction for standardization. Trait data for genetic resources in Japan and France are managed using independently developed standards. The lack of mapping standards hinders data integration and interoperability. To support experts in the mapping process, we developed a tool that translates trait terms. A generative AI-based translation tool appears to be applicable for collecting relevant information to support mapping between trait terms, as well as translating newly submitted Japanese trait terms into English. less than 1 minute read
• Dec 19, 2025

  Increasing FAIRness in agrosystem sciences and plant phenomics

  As part of the de.NBI BioHackathon 2023, we here report about our progress on increasingFAIR-compliance in agrosystem sciences and plant phenomics. Through the collaborative effortsof the agrosystem and plant sciences communities, research data are available through variousdata repositories and infrastructures. To foster these developments and increase the value forthe communities, enabling FAIR-compliance for scientific datasets is one top priority strategicaim. Due to the heterogeneity of the sub-domains and their requirements, we addressedthree challenges with direct relation to specific FAIR principles: Increasing findability of digitalagrosystem resources by extending Schema.org, Enabling easy creation of MIAPPE-compliantISA metadata for Plant Phenotyping Experiments, and Increasing Plant Data Accessibility andCollaboration with FAIDARE. less than 1 minute read
• Dec 17, 2025

  Decoding Complex Genotype-Phenotype Interactions by Discretizing the Genome

  Background: Despite the ease and affordability of genome sequencing in biomedical research, the genetic causes of many diseases or their subtypes remain unknown due to diverse biological mechanisms that complicate genotype-phenotype relationships. Most previous studies have focused on single variants or sets of variants presumed to be directly causal for the disease. However, incomplete penetrance, in which some individuals carry disease-associated variants yet exhibit no phenotype, suggests that these variants, the genomic background and other secondary factors combine to shape the susceptibility to the disease. 1 minute read
• Dec 16, 2025

  BioHackEU25 report: Towards a Robust Validation Service for Data and Metadata in ARC RO-Crates

  Robust validation of both research data and its accompanying metadata is essential for ensuring adherence to FAIR principles. Current approaches often handle these aspects separately, hindering a holistic quality assessment. Building upon previous BioHackathon work establishing ARCs (Annotated Research Context) as RO-Crates (ARC RO-Crate), we aim to develop and demonstrate an integrated validation strategy for FAIR digital objects. It distinguishes between validating the metadata descriptor and the payload data files.For the metadata descriptor, validation will ensure structural and semantic compliance to the base RO-Crate specification and the ARC-ISA family of RO-Crate profiles, using and extending the RO-Crate validator tool.For the payload data files, validation targets the actual content, since data files often require domain-specific structural and value constraints, which requires explicit schema definitions. For this, we will integrate Frictionless for checking data content against community standards (e.g. MIAPPE, as demonstrated in the HORIZON project AGENT). Crucially, this project will also explore mechanisms for specifying expected data structures’ requirements within the ARC RO-Crate itself. This aims to provide a more self-contained description of data, investigating how such internal requirements can be linked to data validation frameworks, complementing the crate’s metadata validation.The overall goal is to provide a powerful, holistic validation mechanism for ARC RO-Crates, enhancing their reliability, trustworthiness, and FAIRness. A MIAPPE-compliant plant phenomics dataset will serve as a use case. This integrated validation approach aims to streamline quality control for researchers and will be packaged as a deployable microservice, offering broad applicability across diverse research workflows. 1 minute read
• Dec 16, 2025

  MCP server tools with RDF shapes

  In this paper, we present the work we have done during the Japan Biohackathon 2025 about implementing MCP servers supported by RDF data shapes to improve natural language interactions with large RDF datasets using SPARQL. less than 1 minute read