Egon Willigh☮gen 🟥
boosted
excited to see @lipidmaps.bsky.social bridging to the #fediverse !
excited to see @lipidmaps.bsky.social bridging to the #fediverse !
Egon Willigh☮gen 🟥
boosted
"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
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
"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
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.
⁂
More from
BioHackrXiv
Egon Willigh☮gen 🟥
boosted
"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
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.
⁂
More from
BioHackrXiv
"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
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.
⁂
More from
BioHackrXiv
#rdf / #linkeddata design / #ontology design questions here to do with Library of Congress relators (a.k.a. MARC relator terms) published as RDF...
Modeling for these terms in RDF seems peculiar in a few respects (to me), but do any of these characteristics have significant implications or drawbacks for data (re)use? Love to hear from library data people, also interested in the perspective of ontologists practicing outside the library domain!
1/6
alcinnz
boosted
#article #ontology #programming #formal #lisp #concrete
https://screwlisp.small-web.org/lispgames/plant-insect-bird-ontology/
Plant Insect Bird practical formal ontology with Leonardo calculus
I revisit my #lispgames #gamejam #gamedev. In this article I create a formal ontology to be a vehicle for my concrete game redux of the jam (which had been lacklustre if technically interesting. Let's be technically interesting and have more lustre this time round.
Thoughts, commentary, ontological guidance gentle and stern if you will please.
![A brightfield emacs partial screenshot showing a fragment of the low-level source of the formal ontology being created
YMMV if you keep reading.
---------------------------------------------------------
-- organisms-kb
[: type kb-index]
[: latest-written "2025-07-13/03:04.+12"]
[: contents <organisms-kb organisms-kb-properties (location: organisms) (location: plants) (location: insects) (location: birds) (location: sensors) (location: world)>]
[: preferred-directory "Organisms/"]
[: nullvalued {purpose namephrase requires mustload removed-entities uses-hostcommands codefiles profile overlay-on overlay-types overlay-own hostinfo indivinfo onto-amend leos-use dont-display sections local-ents latest-archived-entity archivepoint-sequence attrib-converted latest-rearchived}]
---------------------------------------------------------
-- organisms-kb-properties
[: type loadtime-operation]
[: latest-rearchived nil]
(progn (setf (get 'organisms-kb 'init-startup-proc) #'(lambda nil nil))
(setf (get 'organisms-kb 'end-startup-proc) #'(lambda nil nil))
(setf (get 'organisms-kb 'exit-proc) #'(lambda nil nil)))
---------------------------------------------------------
-- (location: organisms)](https://gamerplus.org/system/media_attachments/files/114/844/253/174/440/431/original/f23284879ca23a91.png)
#article #ontology #programming #formal #lisp #concrete
https://screwlisp.small-web.org/lispgames/plant-insect-bird-ontology/
Plant Insect Bird practical formal ontology with Leonardo calculus
I revisit my #lispgames #gamejam #gamedev. In this article I create a formal ontology to be a vehicle for my concrete game redux of the jam (which had been lacklustre if technically interesting. Let's be technically interesting and have more lustre this time round.
Thoughts, commentary, ontological guidance gentle and stern if you will please.