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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 26/09/2026

"DBCLS BioHackathon 2026 report: RDF publication of Marchantia polymorpha gene annotations, and agent-assisted preparation of DDBJ submissions" doi.org/10.37044/osf.io/xev4p_v1 #BH26JP #biohackathon #rdf "First, gene annotations of the liverwort […] [Original post on fediscience.org]

Figure 2: The bisbibenzyl route under salt stress. (a) Pathway schematic with enzyme steps coloured by the strongest induction among the expressed paralogs of that step. (b) log2 fold change of individual genes over a 100 mM NaCl time course, grouped by step.

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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 20/09/2026

"DBCLS BioHackathon 2026 report: Open, Reproducible Extraction of Data-Entity References from the Biomedical Literature – with Entry-Level Resolution via Identifiers.org / TogoID" doi.org/10.37044/osf.io/p87z6_v1 #biohackathon #identifier #BH26JP […] [Original post on fediscience.org]

Figure 3:Data Reuse Dashboard: database usage drill-down

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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 19/09/2026

"DBCLS BioHackathon 2026 report: QPX: Pathway analysis environment for non-model organisms" doi.org/10.37044/osf.io/7egfm_v1 #biohackathon #pathway #bioinformatics #BH26JP #rice #arabidopsis "We report progress on Quest for Pathways with eXpression […] [Original post on fediscience.org]

Part of Figure 1: Arabidopsis-to-rice pathway liftover: whole pathway and N-module detail.

The selection shows the "PathLift" arrow between the original Arabidopsis pathway and the new, pathlifted Oryza sativa pathway. They highlighted a complex with a purple line, which is detailed in the bottom part of the original figure.

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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 18/09/2026

"Building InterMine databases from RDF Portal" doi.org/10.37044/osf.io/dqm3j_v1 #biohackathon #rdf #intermine #BH26JP "The public HumanMine has not had a data release since February 2022. RDF Portal, operated by the Database Division for Life […] [Original post on fediscience.org]

Figure 1:How a mine gets its data. (a) Today each HumanMine source has its own loader, written and maintained as code by the mine’s developers. (b) With RDF Portal and rdfc2im, the work for each dataset moves upstream: RDF Portal holds each dataset’s RDF and an rdf-config model written in rdf-config’s common form, made once and reused by every consumer. rdfc2im is one tool for all sources, and what remains for each source is a curated mapping, kept as data with the evidence for every row. Tags show scope (per source, per dataset, shared, reused), effort (manual, automatic) and form (code, template, data).

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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 18/09/2026

"OSIRIS-MCP: Towards secure conversational access to research information in OSIRIS" doi.org/10.37044/osf.io/36g4c_v3 #biohackathon #osiris #mcp #BH26JP "We developed a prototype Model Context Protocol (MCP) connector for OSIRIS, an open-source […] [Original post on fediscience.org]

Figure 1:Architecture and trust boundaries of OSIRIS MCP. The language-model client communicatesonly with the read-only connector. OSIRIS retains responsibility for permissions, query construction,and access to the authoritative database.

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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 04/09/2026

"AI-Assisted Variant Review Across Asia: Country-Level Expert Panels, Regional Collaboration, and Global Knowledge Sharing" doi.org/10.37044/osf.io/e5g6s_v1 #biohackathon #ai #MHA26 #rareDisease 'We argue that the most useful near-term role of […] [Original post on fediscience.org]

Figure 1. Proposed common platform connecting variant prioritization and evidence organization, structured expert review, and reviewed-knowledge sharing across Asia. In stage 1, integrated evidence sources may include phenotype information, allele frequencies, inheritance, gene-disease context, previous assertions, computational predictions, literature, and functional evidence, yielding a candidate shortlist and a traceable evidence package for review. In stage 2, multidisciplinary reviewers assess evidence in the context of the case, and may accept, reject, modify, or defer individual evidence items while preserving rationale, uncertainty, and disagreement. In stage 3, reviewed records can be reused for country-level operation, regional exchange, and contribution to global knowledge resources. AI and automation support information collection and organization across the workflow, including phenotype structuring, prioritization support, literature retrieval, evidence preparation, retrieval of previous reviews, and re-evaluation support. Final evidence assessment and interpretation remain under expert control.

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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 29/08/2026

"Enhancing e!DAL-PGP: A Modern Data Submission Platform for Plant Science Research Data" doi.org/10.37044/osf.io/9mj78_v1 #biohackathon #BH25DE #fairData #plants "The @deNBI Service e!DAL-PGP (Arend et al., 2016, p. Arend2020) serves as a critical […] [Original post on fediscience.org]

"Figure 3:Screenshot of the 3rd step of the data submission tool for selecting subject." The subject annotations uses various ontologies for the subject terms.

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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 10/08/2026

"4th BioHackathon Germany report: Exploring Gamification Strategies to Enhance Bioinformatics Training" doi.org/10.37044/osf.io/dfwm9_v1 #biohackathon #BH25DE #gamification #training "While gamification can enhance engagement, implementing it […] [Original post on fediscience.org]

Pastel-colored infographic with a circle in the middle with the text "Gamifying Life Sciences Education: 10 Simple Rules", and around that a rectangle with 10 sections radiating our from the central circle, like a pie slice, but then from a rectangular cake. Each section has one of the 10 rules. But for that I refer to the article.

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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 10/08/2026

"Variant representation in RDF" doi.org/10.37044/osf.io/jazsb_v1 "we detected an emerging number of novel RDF models to represent variant information in genomic datasets potentially hindering data reuse. We tackled the question how semantic […] [Original post on fediscience.org]

Figure 1:Illustration of the SemBeacon RDF model mapping to GA4GH VRS RDF model.

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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 27/07/2026

"Measure before you rewrite: ablation-driven redesign of LLM-facing RDF schema documentation in TogoMCP" 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 […] [Original post on fediscience.org]

Figure 2: The v2.3 format’s eleven author-function sections mapped onto v3’s five need-based parts.shape_expressions and sample_rdf_entries do not survive as sections at all: a verified example subsumes both.

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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 10/07/2026

"Maintaining and refining the Tidyomics ecosystem: enhancing core packages and interoperability for EuroBioc2026" doi.org/10.37044/osf.io/cd9s6_v1 "First, we introduce tidyAnnData, a new package that expands interoperability between the tidyverse and […] [Original post on fediscience.org]

Figure 1: Schematic representation of the Tidyomics hackathon aims. 1. We introduced tidyAnnData to provide tidy operators for AnnData objects; 2. We fixed major bugs in information accessibility for Tidyomics core packages; 3. We updated and extended Tidyomics packages such as DFplyr and tidybulk; 4. We provide a comprehensive and concise vignette for the tidySingleCellExperiment package. This plot was created by Google Nano Banana 2.

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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 27/06/2026

BioHackrXiv authors can use Citation Typing Ontology (CiTO) citation intent annotations to express why they are citing the articles they cite. And many have! See doi.org/10.37044/OSF.IO/6RJVC and doi.org/10.5281/ZENODO.10072013 With 2026 […] [Original post on fediscience.org]

network of nodes and edges, with each node being a BioHackrXiv preprint, and the edges citations with CiTO intent annotations. The nodes have the first author surname and publication year, and the edges have the label of the CiTO citation intent. The graph has a few isolated networks, and 30 nodes in totel. The largest network has 17 articles and their 21 citations between these preprints.

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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 15/06/2026

"Bioconductor Spatial Data and Image Analysis Hackathon" doi.org/10.37044/osf.io/9ej32_v1 "We report the outcomes of the Bioconductor Spatial Data and Image Analysis Hackathon, held in Venice, Italy in April 2026. Twenty-seven researchers and […] [Original post on fediscience.org]

One of the figures from the preprint. It shows a 2d image of tissue, colored with a red stain, showing the red and white image that we see. At the top there is the text "Overlay: Terra Image and Segmentation".

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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 07/06/2026

"2nd SpatialData Hackathon: Frameworks, Formats and Interoperability" doi.org/10.37044/osf.io/s6bph_v1 "The event gathered experts to advance spatial omics through four hackathon tracks: (i) R interoperability, (ii) accessibility and performance of […] [Original post on fediscience.org]

Figure 1: Comparison of Zarr, bioimaging and single-cell/spatial omics packages across scverse and Bioconductor ecosystems that interface with SpatialData objects on disk (“Database-icon” by Zahra Ibrahem is licensed under CC BY-SA 4.0. To view a copy of this license, visit https://creativecommons.org/licenses/by-sa/4.0/?ref=openverse.)

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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 22/05/2026

"INTOXICOM Workshop Report: Systems Biology Models for Toxicology" doi.org/10.37044/osf.io/zf2qj_v1 "The workshop took place under the INTOXICOM Implementation Study workshop series (Integrating the toxicology community into ELIXIR 2024) and aimed to […] [Original post on fediscience.org]

Schematic with many boxes in various UML types. At the top we see a purple box with various stakeholders (JRC, ELIXIR, OECD, EIRENE, NWO, etc), and a blue box below this with various activities (AOP Wiki, Omics AOP, Methods AOP, AOP-DB, AOPXplorer, etc), supported by a layer reflection data warehouses (without much details). On the right side we see three headers (Macro level: landscape, Meso level: regimes, and Micro level (niches).

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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 14/04/2026

"Improving package annotation in metabolomics andproteomics via robust, ontology-driven LLM integration" doi.org/10.37044/osf.io/x5v6b_v1 "At BioHackathon Europe 2025, our team explored how Large Language Models (LLMs) can assist this process through […] [Original post on fediscience.org]

Figure 1: Mid-week reporting poster used during BioHackathon Europe 2025 to communicate early design decisions, illustrate EDAM branches, and motivate the use of the Model Context Protocol to mitigate LLM hallucinations during ontology-driven tool annotation.

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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 21/03/2026

"Towards Federated Learning Across Biobanks: Prototype Software from the 2026 Carnegie Mellon University–NVIDIA Hackathon" doi.org/10.37044/osf.io/5psfj_v1 "The Carnegie Mellon University-NVIDIA Federated Learning Hackathon for Biomedical […] [Original post on fediscience.org]

Figure 2.10-1: Distribution of species and proteins across different taxa (Human, Virus, Prokaryote, Eukaryote) in the ProteinGym benchmark.

It shows each of the four in separate colorful boxplots. Not easy to explain, and plz read the article for the details.

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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 25/02/2026

"Bidirectional bridge: GitHub ⇄ bio.tools" doi.org/10.37044/osf.io/8ktd6_v1 "Here, we describe the tooling for a bidirectional bridge between the software developmentplatform GitHub and the ELIXIR bio.tools registry of life sciences software tools […] [Original post on fediscience.org]

Figure 3:Principal component analysis (PCA) of bio.tools entries with a GitHub repository basedon the numbers of contributors, forks (and network count), commits, pulls, releases, open issues,subscribers, watchers, stargazers and the average time to close issues. The colors represent thebio.toolsmaturitylevel, i.e.,Emerging,MatureorLegacy.

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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 31/01/2026

"BH25DE report: On the path to machine-actionabletraining materials" doi.org/10.37044/osf.io/un6cd_v1 "We demonstrated contentfederationvia themTeSS-Xplatform, enabling cross-instanceexchange and preparing for future integration with the EOSC […] [Original post on fediscience.org]

Figure 1: Curated crosswalks between MoDALIA and Schema.org metadata models for training materials.

The figure shows schema.org on the left side, SSSOM icon below an bidirectional arrow in the middle in a screenshot of a MoDALIA predicate definition on the right.

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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 22/01/2026

"BioHackEU25 report: METRICS - Monitoring of KeyPerformance Indicators for ELIXIR Services" 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 […] [Original post on fediscience.org]

Part of Figure 1:Photo of project poster for the mid-week presentation. The photo shows a A0 sheet notes from the meeting, including country flags, some key words, and the output of brainstorming.

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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 06/01/2026

"QPX: Pathway analysis environment" doi.org/10.37044/osf.io/m37f2_v1 "Building on our work at DBCLS BioHackathon 2023 (BH23), where we introduced QPX andpromoted pathway modeling with WikiPathways (Pico et al., 2008) using PathVisio (Kutmon etal […] [Original post on fediscience.org]

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