#bh25jp — Public Fediverse posts

"Variant annotation in RDF for clinical trials matching" https://doi.org/10.37044/osf.io/2hbqf_v1

#biohackathon #BH25JP #rdf #clinicalTrial

"Precision oncology depends on semantic, interoperable representations of genomic variants (GV) - particularly structural variants (SVs) - to match patients with clinical trials. In this exploratory project, we investigated the use of RDF and the GA4GH VRS Schema to standardize variant annotations and integrate them with clinical trial data. Our work, developed in collaboration with the Pangenome Graphs and Platform for Precision Medicine groups, prototypes an RDF-based data harmonization that paves the way for improved semantic interoperability in precision medicine, especially for cancer research and AI-driven discovery." https://index.biohackrxiv.org/2026/08/09/2hbqf.html

"Measure before you rewrite: ablation-driven redesign of LLM-facing RDF schema documentation in TogoMCP" https://doi.org/10.37044/osf.io/6v5ra_v1

#biohackathon #BH25JP #llm #mcp

"MIE files are per-database YAML documents that TogoMCP supplies to a large language model at query time so it can compose SPARQL against the DBCLS RDF Portal. Ours had grown to eleven sections, semi-automatically generated for each of 36 databases and reviewed by hand." http://index.biohackrxiv.org/2026/07/26/6v5ra.html

"QPX: Pathway analysis environment" https://doi.org/10.37044/osf.io/m37f2_v1

"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 etal., 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." https://osf.io/m37f2_v1

#biohackathon #BH25JP #wikipathways

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

"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

"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

three more #BH25JP reports are now online: https://index.biohackrxiv.org/tag/BH25JP

- "AI in Practice: Insights from a Community Survey of Biohackathon Participants" https://doi.org/10.37044/osf.io/pza7v_v1
- "on2vec: Ontology Embeddings with Graph Neural Networks and Sentence Transformers" https://doi.org/10.37044/osf.io/4f763_v1
- "DBCLS BioHackathon 2025 report on the WikiBlitz" https://doi.org/10.37044/osf.io/7s6da_v1

five new species, five new pathways, five ways caffeine is synthesized:

- Theobroma cacao caffeine synthesis (WP5588): https://www.wikipathways.org/pathways/WP5588.html
- Citrus sinensis caffeine synthesis (WP5589): https://www.wikipathways.org/pathways/WP5589.html
- Paullinia cupana caffeine synthesis (WP5590): https://www.wikipathways.org/pathways/WP5590.html
- Ilex paraguariensis caffeine synthesis (WP5591): https://www.wikipathways.org/pathways/WP5591.html
- Coffea arabica caffeine synthesis (WP5586): https://www.wikipathways.org/pathways/WP5586.html

#BH25JP

I "added" DOI support to the BioHackrXiv Index, so that I now can extract DOIs from preprints and put them in the index. With CiTO annotation that also shows up in the JSON feed :) For example, for this #BH25JP preprint https://doi.org/10.37044/osf.io/8kap3_v1 this looks like this: https://index.biohackrxiv.org/2025/09/30/8kap3.html

#preprint #biohackathon

the first four #BH25JP preprints have appeared in BioHackRxiv: https://index.biohackrxiv.org/

This includes "Creation and Publication Analytical Workflow of Creators' Interests" https://doi.org/10.37044/osf.io/qd5sz_v1 and "A Lightweight PURL Resolver for Linked Life Science Data" https://doi.org/10.37044/OSF.IO/8KAP3_V1 both with CiTO annotations