#Tag · bonfire.cafe

Very nice fediverse-powered coverage of the European Biohackathon #BioHackEU25 at https://guide.biohackrxiv.org/fediwall/

Thanks @biohackrxiv !

Fediwall

Egon Willigh☮gen 🟥 boosted

BioHackrXiv

@biohackrxiv@fediscience.org · 8 hours ago

"BioHackEU25 Report Project 16: MiCoReCa (Microbiome Community Resource Catalogue) - Towards Centralized Curation And Integration Of Microbiome Bioinformatics Resources" https://doi.org/10.37044/osf.io/jfpsx_v1

"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." https://index.biohackrxiv.org/2025/12/31/jfpsx.html

#biohackathon #elixireurope #BIoHackEU25

BioHackrXiv Preprints

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of numerous bioinformatics tools and databases, but information about them remains fragmented across disparate, often outdated cataloging efforts, hindering resource discovery and utilization.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.

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BioHackrXiv

@biohackrxiv@fediscience.org · 8 hours ago

#biohackathon #elixireurope #BIoHackEU25

BioHackrXiv Preprints

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

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BioHackrXiv

Egon Willigh☮gen 🟥 boosted

BioHackrXiv

@biohackrxiv@fediscience.org · 2 weeks ago

"BioHackEU25 report: Towards a Robust ValidationService for Data and Metadata in ARC RO-Crates" https://doi.org/10.37044/osf.io/zah28_v1

"For the metadata, validation will ensure structural and semantic compliance to the base RO-Crate specification and the ARC family of RO-Crate profiles, including the ISA, Workflow-Runand Datamap profiles, using and extending therocrate-validatortool,which uses SHACL (Shapes Constraint Language) and Python to validateRO-Crate metadata." http://index.biohackrxiv.org/2025/12/16/zah28.html

#biohackEU25

BioHackrXiv Preprints

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.

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BioHackrXiv

@biohackrxiv@fediscience.org · 2 weeks ago

"BioHackEU25 report: Towards a Robust ValidationService for Data and Metadata in ARC RO-Crates" https://doi.org/10.37044/osf.io/zah28_v1

#biohackEU25

BioHackrXiv Preprints

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

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BioHackrXiv

Christian Meesters and 1 other boosted

BioHackrXiv

@biohackrxiv@fediscience.org · last month

"Mining the potential of knowledge graphs for metadata on training" https://doi.org/10.37044/osf.io/gv2ac_v1

"A dedicated pipeline parses RDF/Turtle dumps, deduplicates entries, and builds rich indexes (keyword, provider, location, date, topic) that power a Model Context Protocol (MCP) server. The MCP offers live and offline search tools—including keyword, provider, location, date, topic, and SPARQL queries" https://index.biohackrxiv.org/2025/11/29/gv2ac.html

#biohackathon #BioHackEU25 #BH25EU #SPARQL #MCP

BioHackrXiv

@biohackrxiv@fediscience.org · last month

"Mining the potential of knowledge graphs for metadata on training" https://doi.org/10.37044/osf.io/gv2ac_v1

#biohackathon #BioHackEU25 #BH25EU #SPARQL #MCP

Wolfgang Maier

@zerodivision@fediscience.org · 2 months ago

Very nice fediverse-powered coverage of the European Biohackathon #BioHackEU25 at https://guide.biohackrxiv.org/fediwall/

Thanks @biohackrxiv !

Fediwall

Egon Willigh☮gen 🟥 boosted

BioHackrXiv

@biohackrxiv@fediscience.org · 2 months ago

"Accelerating open science – the impact of BioHackathon Europe" https://elixir-europe.org/news/BH2025

"To date, 43 preprints have been published on the outcomes of BioHackathon Europe projects, with a combined total of over 14,000 downloads – clear evidence of their value and influence. The two most popular papers are Knowledge graphs and wikidata subsetting (2020) with 1268 downloads and Infrastructure for synthetic health data (2022) with 1087 downloads."

#BioHackEU25

Accelerating open science – the impact of BioHackathon Europe | ELIXIR

BioHackrXiv

@biohackrxiv@fediscience.org · 2 months ago

"Accelerating open science – the impact of BioHackathon Europe" https://elixir-europe.org/news/BH2025

#BioHackEU25

Accelerating open science – the impact of BioHackathon Europe | ELIXIR