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Egon Willigh☮gen 🟥 boosted

@biohackrxiv@fediscience.org · 4 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of numerous bioinformatics tools and databases, but information about them remains fragmented across disparate, often outdated cataloging efforts, hindering resource discovery and utilization.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@fediscience.org · 4 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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Christian Meesters and 1 other boosted

@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

Egon Willigh☮gen 🟥 boosted

@biohackrxiv@fediscience.org · last month

"A Blueprint for Open Science: How Transatlantic Teams Built and Deployed Knowledge Graphs to Enable Biological (AI) Models" https://doi.org/10.37044/osf.io/g4rk2_v1

"these projects and pipelines showcase methods for constructing KGs from existing biomedical datasets andexemplify the practical deployment of GraphRAG in real-world biomedical context, thereby advancing the biomedical sciences [..]" https://index.biohackrxiv.org/2025/11/26/g4rk2.html

#biohackathon #KGhack25 #KGhack #openscience #AWSOpen

Egon Willigh☮gen 🟥 boosted

@biohackrxiv@fediscience.org · last month

"BioHackEU25 report: Scop3PTM Next - Interactive visualization of PTM data across sequence, structure and interactions" https://doi.org/10.37044/osf.io/xvrud_v1

"Scop3PTM Next was developed during BioHackathon Europe 2025 to address the need for integrated visualization of protein-centric data across sequence (and modification), interaction and structural contexts." https://index.biohackrxiv.org/2025/11/26/xvrud.html

#BioHack25EU #biohackathon #protein #bioinformatics

@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@fediscience.org · last month

"A Blueprint for Open Science: How Transatlantic Teams Built and Deployed Knowledge Graphs to Enable Biological (AI) Models" https://doi.org/10.37044/osf.io/g4rk2_v1

"these projects and pipelines showcase methods for constructing KGs from existing biomedical datasets andexemplify the practical deployment of GraphRAG in real-world biomedical context, thereby advancing the biomedical sciences [..]" https://index.biohackrxiv.org/2025/11/26/g4rk2.html

#biohackathon #KGhack25 #KGhack #openscience #AWSOpen

@biohackrxiv@fediscience.org · last month

"BioHackEU25 report: Scop3PTM Next - Interactive visualization of PTM data across sequence, structure and interactions" https://doi.org/10.37044/osf.io/xvrud_v1

"Scop3PTM Next was developed during BioHackathon Europe 2025 to address the need for integrated visualization of protein-centric data across sequence (and modification), interaction and structural contexts." https://index.biohackrxiv.org/2025/11/26/xvrud.html

#BioHack25EU #biohackathon #protein #bioinformatics

@biohackrxiv@fediscience.org · last month

Call for Biohackathon topics: "SWAT4HCLS Biohackathon 2026, Amsterdan, The Netherlands" https://www.swat4ls.org/swat4hcls-biohackathon-2026/

#biohackathon #swat4hcls26 #swat4hcls

Egon Willigh☮gen 🟥 boosted

@biohackrxiv@fediscience.org · 2 months ago

"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

@biohackrxiv@fediscience.org · 2 months ago

"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

Egon Willigh☮gen 🟥 boosted

@biohackrxiv@fediscience.org · 2 months ago

"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

BioHackrXiv Preprints

on2vec: Ontology Embeddings with Graph Neural Networks and Sentence Transformers

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.

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@biohackrxiv@fediscience.org · 2 months ago

"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

BioHackrXiv Preprints

on2vec: Ontology Embeddings with Graph Neural Networks and Sentence Transformers

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.

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Egon Willigh☮gen 🟥 boosted

@biohackrxiv@fediscience.org · 2 months ago

"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

BioHackrXiv Preprints

AI in Practice: Insights from a Community Survey of Biohackathon Participants

Understanding the practical application of artificial intelligence (AI) in research is increasingly important as it becomes embedded in life sciences and bioinformatics. This paper reports on a multilingual survey, developed through community discussions at the 2025 BioHackathon in Japan and distributed through its networks, to capture current practices, successes, and challenges in AI adoption. The survey, oﬀered in English, Japanese, and Thai, received 105 responses spanning diverse demographics, regions, and professional backgrounds. 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. Successes were noted in eﬃciency, coding support, and proposal writing, whereas challenges centered on accuracy and reliability. Institutional support emerged as a key factor: respondents in Japan, Thailand, and the private sector reported stronger support and higher satisfaction than English-speaking or academic counterparts. By documenting real-world practices and concerns, this survey provides a valuable community-driven resource to guide responsible AI development and foster international collaboration in bioinformatics.

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@biohackrxiv@fediscience.org · 2 months ago

"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

BioHackrXiv Preprints

AI in Practice: Insights from a Community Survey of Biohackathon Participants

Understanding the practical application of artificial intelligence (AI) in research is increasingly important as it becomes embedded in life sciences and bioinformatics. This paper reports on a multilingual survey, developed through community discussions at the 2025 BioHackathon in Japan and distributed through its networks, to capture current practices, successes, and challenges in AI adoption. The survey, oﬀered in English, Japanese, and Thai, received 105 responses spanning diverse demographics, regions, and professional backgrounds. 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. Successes were noted in eﬃciency, coding support, and proposal writing, whereas challenges centered on accuracy and reliability. Institutional support emerged as a key factor: respondents in Japan, Thailand, and the private sector reported stronger support and higher satisfaction than English-speaking or academic counterparts. By documenting real-world practices and concerns, this survey provides a valuable community-driven resource to guide responsible AI development and foster international collaboration in bioinformatics.

⁂

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Egon Willigh☮gen 🟥 boosted

@biohackrxiv@fediscience.org · 2 months ago

"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

BioHackrXiv Preprints

Translating and Formalizing the MIRAGE Guidelines to a Prototype MIRAGE Ontology and DCAT3 Extension Vocabulary for Glycomics Data Management

The Minimum Information Required for A Glycomics Experiment (MIRAGE) guidelines have established comprehensive reporting standards for glycomics research, yet their implementation in semantic web technologies remains limited. 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. The complementary MIRAGE-DCAT3 vocabulary extends W3C DCAT3 with glycomics-specific metadata properties for dataset cataloging and discovery. Our implementation addresses critical challenges in glycomics data interoperability through comprehensive mappings to established ontologies including GlycoRDF, PSI-MS, and DCTERMS. This semantic framework enables automated quality assessment, federated data querying, and enhanced reproducibility in glycomics research, supporting broader adoption of FAIR principles in the glycobiology community. The framework demonstrates comprehensive coverage of MIRAGE reporting requirements across multiple analytical platforms including mass spectrometry, liquid chromatography, capillary electrophoresis, NMR spectroscopy, and lectin microarray analysis.

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@biohackrxiv@fediscience.org · 2 months ago

"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

BioHackrXiv Preprints

Translating and Formalizing the MIRAGE Guidelines to a Prototype MIRAGE Ontology and DCAT3 Extension Vocabulary for Glycomics Data Management

The Minimum Information Required for A Glycomics Experiment (MIRAGE) guidelines have established comprehensive reporting standards for glycomics research, yet their implementation in semantic web technologies remains limited. 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. The complementary MIRAGE-DCAT3 vocabulary extends W3C DCAT3 with glycomics-specific metadata properties for dataset cataloging and discovery. Our implementation addresses critical challenges in glycomics data interoperability through comprehensive mappings to established ontologies including GlycoRDF, PSI-MS, and DCTERMS. This semantic framework enables automated quality assessment, federated data querying, and enhanced reproducibility in glycomics research, supporting broader adoption of FAIR principles in the glycobiology community. The framework demonstrates comprehensive coverage of MIRAGE reporting requirements across multiple analytical platforms including mass spectrometry, liquid chromatography, capillary electrophoresis, NMR spectroscopy, and lectin microarray analysis.

⁂

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Egon Willigh☮gen 🟥 boosted

@biohackrxiv@fediscience.org · 2 months ago

our preview website has been revamped: https://preview.biohackrxiv.org/

#biohackrxiv #preprint #biohackathon

@biohackrxiv@fediscience.org · 2 months ago

our preview website has been revamped: https://preview.biohackrxiv.org/

#biohackrxiv #preprint #biohackathon

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