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/

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/

"MCP server tools with RDF shapes" https://doi.org/10.37044/osf.io/8qeh5_v1

"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." https://index.biohackrxiv.org/2025/12/16/8qeh5.html

#BH25JP #MCP #SPARQL

"MCP server tools with RDF shapes" https://doi.org/10.37044/osf.io/8qeh5_v1

"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." https://index.biohackrxiv.org/2025/12/16/8qeh5.html

#BH25JP #MCP #SPARQL

"DBCLS BioHackathon 2025 report on the WikiBlitz" https://doi.org/10.37044/osf.io/7s6da_v1

"As part of the DBCLS BioHackathon 2025, we organized a WikiBlitz to improve biodiversity knowledge by integrating iNaturalist, GBIF, Wikidata, and Wikipedia. Participants identified local flora and fauna, filling gaps in multilingual Wikipedia articles. This report summarizes the methodology, results, and insights, illustrating the usefulness of combining citizen science with digital platforms to enrich ecological data and promote biodiversity awareness." https://index.biohackrxiv.org/2025/10/24/7s6da.html

By @Andrawaag et al.

#biohackathon #bh25jp #wikidata #inaturalist #wikiblitz

"DBCLS BioHackathon 2025 report on the WikiBlitz" https://doi.org/10.37044/osf.io/7s6da_v1

"As part of the DBCLS BioHackathon 2025, we organized a WikiBlitz to improve biodiversity knowledge by integrating iNaturalist, GBIF, Wikidata, and Wikipedia. Participants identified local flora and fauna, filling gaps in multilingual Wikipedia articles. This report summarizes the methodology, results, and insights, illustrating the usefulness of combining citizen science with digital platforms to enrich ecological data and promote biodiversity awareness." https://index.biohackrxiv.org/2025/10/24/7s6da.html

By @Andrawaag et al.

#biohackathon #bh25jp #wikidata #inaturalist #wikiblitz

"on2vec: Ontology Embeddings with Graph Neural Networks and Sentence Transformers" https://doi.org/10.37044/osf.io/4f763_v1

"Ontologies provide structured vocabularies and relationships essential for organizing biological knowledge, yet their symbolic nature limits integration with modern machine learning methods. Leveraging recent advances in graph neural networks (GNNs) and transformer-based language models, we present on2vec, a toolkit developed during the DBCLS BioHackathon 2025 for generating vector embeddings from OWL ontologies. on2vec integrates structural information from ontology hierarchies with semantic features from textual annotations using HuggingFace Sentence Transformers, producing domain-aware embeddings suitable for downstream biomedical applications and ontology-based reasoning tasks." https://index.biohackrxiv.org//2025/10/21/4f763.html

#biohackathon #ontology #BH25JP

"on2vec: Ontology Embeddings with Graph Neural Networks and Sentence Transformers" https://doi.org/10.37044/osf.io/4f763_v1

"Ontologies provide structured vocabularies and relationships essential for organizing biological knowledge, yet their symbolic nature limits integration with modern machine learning methods. Leveraging recent advances in graph neural networks (GNNs) and transformer-based language models, we present on2vec, a toolkit developed during the DBCLS BioHackathon 2025 for generating vector embeddings from OWL ontologies. on2vec integrates structural information from ontology hierarchies with semantic features from textual annotations using HuggingFace Sentence Transformers, producing domain-aware embeddings suitable for downstream biomedical applications and ontology-based reasoning tasks." https://index.biohackrxiv.org//2025/10/21/4f763.html

#biohackathon #ontology #BH25JP

"AI in Practice: Insights from a Community Survey of Biohackathon Participants" https://doi.org/10.37044/osf.io/pza7v_v1

"Findings reveal that most participants are frequent AI users, with tools like ChatGPT, Gemini, and Claude widely adopted, with ChatGPT as number one response. AI is primarily used to assist or draft tasks in coding, research, and writing, while full task automation remains uncommon, reflecting a preference for AI as a collaborative aid rather than a replacement." https://index.biohackrxiv.org//2025/10/12/pza7v.html

#biohackathon #AI #BH25JP

"AI in Practice: Insights from a Community Survey of Biohackathon Participants" https://doi.org/10.37044/osf.io/pza7v_v1

"Findings reveal that most participants are frequent AI users, with tools like ChatGPT, Gemini, and Claude widely adopted, with ChatGPT as number one response. AI is primarily used to assist or draft tasks in coding, research, and writing, while full task automation remains uncommon, reflecting a preference for AI as a collaborative aid rather than a replacement." https://index.biohackrxiv.org//2025/10/12/pza7v.html

#biohackathon #AI #BH25JP

"Translating and Formalizing the MIRAGE Guidelines to a Prototype MIRAGE Ontology and DCAT3 Extension Vocabulary for Glycomics Data Management" https://doi.org/10.37044/osf.io/wj8bz_v1

"We present the first comprehensive semantic formalization of MIRAGE guidelines through an integrated RDF ontology framework comprising the MIRAGE Ontology and MIRAGE-DCAT3 vocabulary. The MIRAGE Ontology models glycan structures, biological specimens, analytical instruments, and experimental processes with formal OWL semantics and SHACL validation constraints." https://index.biohackrxiv.org//2025/09/30/wj8bz.html

#biohackathon #BH25JP #shacl #ontology

"Translating and Formalizing the MIRAGE Guidelines to a Prototype MIRAGE Ontology and DCAT3 Extension Vocabulary for Glycomics Data Management" https://doi.org/10.37044/osf.io/wj8bz_v1

"We present the first comprehensive semantic formalization of MIRAGE guidelines through an integrated RDF ontology framework comprising the MIRAGE Ontology and MIRAGE-DCAT3 vocabulary. The MIRAGE Ontology models glycan structures, biological specimens, analytical instruments, and experimental processes with formal OWL semantics and SHACL validation constraints." https://index.biohackrxiv.org//2025/09/30/wj8bz.html

#biohackathon #BH25JP #shacl #ontology