#biohackeu25 — Public Fediverse posts

"Minimal information standardization of phenomic experimental data in animals" https://doi.org/10.37044/osf.io/ncrkm_v1

"The current landscape of animal phenomics is characterized by a substantial lack of stan-dardization, hindering data reuse, reproducibility, and interoperability across studies, all ofwhich are particularly important in light of the 3Rs principles for animal experiments (replace, reduce, refine) (Hubrecht & Carter, 2019). Within ELIXIR, the Domestic Animals Genome andPhenome Focus Group (since December 2025 an ELIXIR community) emerged to establishstandardized practices that enhance the quality and interoperability of animal research data" http://index.biohackrxiv.org/2026/04/10/ncrkm.html

#phenomics #3r #biohackathon #BioHackEU25

"BioHackEU25 report: METRICS - Monitoring of KeyPerformance Indicators for ELIXIR Services" https://doi.org/10.37044/osf.io/2jgk4_v1

"As part of the BioHackathon Europe 2025, we report on the activities of the METRICS project, which addresses the need for consistent and transparent evaluation of services across ELIXIR and related initiatives using KPIs. The project brings together experts from multiple ELIXIR Nodes and scientific domains to identify, harmonise, and semantically model KPIs that reflect service quality, usage, sustainability, and impact."

#ELIXIREurope #BioHackathon #BioHackEU25

2025 has come to an end. This year, we published 45 preprints resulting from 16 different biohackathons. Sometimes reports come in late, as we will see. A quick list of #biohackathon meetings with preprints in 2025:

- DBCLS BioHackathon 2023 #BH23JP: https://index.biohackrxiv.org/tag/BH23JP
- DBCLS BioHackathon 2024 #BH24JP: https://index.biohackrxiv.org/tag/BH24JP
- DBCLS BioHackathon 2025 #BH25JP: https://index.biohackrxiv.org/tag/BH25JP

- BioHackathon Europe 2023 #BH23EU: https://index.biohackrxiv.org/tag/BH23EU
- BioHackathon Europe 2024 #BH24EU: https://index.biohackrxiv.org/tag/BH24EU
- BioHackathon Europe 2025 #BioHackEU25: https://index.biohackrxiv.org/tag/BioHackEU25

- 2nd BioHackathon Germany 2023 #BH23DE: https://index.biohackrxiv.org/tag/BH23DE
- 3rd BioHackathon Germany 2024 #BH24DE: https://index.biohackrxiv.org/tag/BH24DE

- 16th International SWAT4HCLS Conference 2025 #SWAT4HCLS25: https://index.biohackrxiv.org/tag/SWAT4HCLS25

And seven others! A full overview is found on this page: https://index.biohackrxiv.org/meetings/

"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

"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

"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

The last night of the Biohackathon is coming to a close, and the karaoke music drifts down to the lakeside #biohackeu25 #fullmoon

Lots of fun making a chain reaction at #biohackeu25

#BioHackEU25 Last week Vedran and Matúš visited me for a head start on this week's BioHackathon. We were kindly hosted by Dr. Sven Twardziok at Charité/BIH. With Vedran we dug into the cwljava library and after I made several fixes he opened https://github.com/sanctuuary/APE/pull/138
To follow on with that I will be finally releasing the cwljava library on the Maven Central Repository.
With Matúš we discussed the ongoing work to expand the edamontology.org to more domains, specifically Earth Observation / Geo. He showed me some previous unreleased work and we scheduled a meeting for today with Lorenz Grouper and colleagues, whom I was recently introduced to by Iacopo Colonnelli as part of our CWL4HPC work.

"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

Project 14 here at the #BioHackEU25 will work to assess and improve the state of #mzTab-M for #Metabolomics over the next few days. Plus having fun meeting all the other attendees here near Berlin

the BioHackathon Europe is coming very near now :)

#BioHackEU25