#Tag · bonfire.cafe

Christian Meesters and 1 other boosted

@biohackrxiv@fediscience.org · last week

"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 week

"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 · 2 weeks ago

"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 week

"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 week

"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 · 2 weeks ago

"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 · 3 weeks ago

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 · last month

"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 · last month

"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 · last month

"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 · last month

"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 · last month

"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 · last month

"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 · last month

"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 · last month

"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 · last month

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

#biohackrxiv #preprint #biohackathon

@biohackrxiv@fediscience.org · last month

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

#biohackrxiv #preprint #biohackathon

Egon Willigh☮gen 🟥 boosted

@biohackrxiv@fediscience.org · last month

"Leveraging RDF and CURIE metadata resolution with identifiers.org" https://doi.org/10.37044/osf.io/xza73_v1

"Identifiers.org provides two core services for CURIEs in life sciences. One is a registry of CURIE prefixes and URL locations that contain entries for the main life sciences datasets. The other is a resolver that allows for consistent data access using registry information to redirect to current URLs for CURIE identifiers. For this work, we aimed to expand these services to facilitate the integration of CURIE-related metadata into different contexts." https://index.biohackrxiv.org//2025/06/02/xza73.html

#biohackathon #BH24EU

BioHackrXiv Preprints

Leveraging RDF and CURIE metadata resolution with identifiers.org

Identifiers.org provides two core services for CURIEs in life sciences. One is a registry of CURIE prefixes and URL locations that contain entries for the main life sciences datasets. The other is a resolver that allows for consistent data access using registry information to redirect to current URLs for CURIE identifiers. For this work, we aimed to expand these services to facilitate the integration of CURIE-related metadata into different contexts. The first part of this exports the registry in RDF with a SPARQL server to allow queries on the dataset. Through these, RDF-based systems can associate with registry metadata on different data collections. Allowing, for example, services that have identifiers.org URLs to collect metadata on the collection that it references. The second part expands on the existing metadata resolver to be able to collect CURIE-related metadata from different metadata providers.While the previous resolver could only collect LDJSON notations from pages, it can now be expanded to collect from any metadata provider.For this work, we implement two proof of concept retrievers, one for EBI Search, a text search engine that allows for metadata acquisition, and one for TogoID, an ID mapping service for life sciences.Finally, we gather some future tasks for identifiers.org services.

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@biohackrxiv@fediscience.org · last month

"Leveraging RDF and CURIE metadata resolution with identifiers.org" https://doi.org/10.37044/osf.io/xza73_v1

"Identifiers.org provides two core services for CURIEs in life sciences. One is a registry of CURIE prefixes and URL locations that contain entries for the main life sciences datasets. The other is a resolver that allows for consistent data access using registry information to redirect to current URLs for CURIE identifiers. For this work, we aimed to expand these services to facilitate the integration of CURIE-related metadata into different contexts." https://index.biohackrxiv.org//2025/06/02/xza73.html

#biohackathon #BH24EU

BioHackrXiv Preprints

Leveraging RDF and CURIE metadata resolution with identifiers.org

Identifiers.org provides two core services for CURIEs in life sciences. One is a registry of CURIE prefixes and URL locations that contain entries for the main life sciences datasets. The other is a resolver that allows for consistent data access using registry information to redirect to current URLs for CURIE identifiers. For this work, we aimed to expand these services to facilitate the integration of CURIE-related metadata into different contexts. The first part of this exports the registry in RDF with a SPARQL server to allow queries on the dataset. Through these, RDF-based systems can associate with registry metadata on different data collections. Allowing, for example, services that have identifiers.org URLs to collect metadata on the collection that it references. The second part expands on the existing metadata resolver to be able to collect CURIE-related metadata from different metadata providers.While the previous resolver could only collect LDJSON notations from pages, it can now be expanded to collect from any metadata provider.For this work, we implement two proof of concept retrievers, one for EBI Search, a text search engine that allows for metadata acquisition, and one for TogoID, an ID mapping service for life sciences.Finally, we gather some future tasks for identifiers.org services.

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