Tootfinder

The Cell Ontology in the age of single-cell omics
Shawn Zheng Kai Tan, Aleix Puig-Barbe, Damien Goutte-Gattat, Caroline Eastwood, Brian Aevermann, Alida Avola, James P Balhoff, Ismail Ugur Bayindir, Jasmine Belfiore, Anita Reane Caron, David S Fischer, Nancy George, Benjamin M Gyori, Melissa A Haendel, Charles Tapley Hoyt, Huseyin Kir, Tiago Lubiana, Nicolas Matentzoglu, James A Overton, Beverly Peng, Bjoern Peters, Ellen M Quardokus, Patrick L Ray, Paola Roncaglia, Andrea D Rivera, Ra…

The Cell Ontology in the age of single-cell omics
Single-cell omics technologies have transformed our understanding of cellular diversity by enabling high-resolution profiling of individual cells. However, the unprecedented scale and heterogeneity of these datasets demand robust frameworks for data integration and annotation. The Cell Ontology (CL) has emerged as a pivotal resource for achieving FAIR (Findable, Accessible, Interoperable, and Reusable) data principles by providing standardized, species-agnostic terms for canonical cell types - …

An Ontology for Representing Curriculum and Learning Material
Antrea Christou, Chris Davis Jaldi, Joseph Zalewski, Hande K\"u\c{c}\"uk McGinty, Pascal Hitzler, Cogan Shimizu
https://arxiv.org/abs/2506.05751

An Ontology for Representing Curriculum and Learning Material
Educational, learning, and training materials have become extremely commonplace across the Internet. Yet, they frequently remain disconnected from each other, fall into platform silos, and so on. One way to overcome this is to provide a mechanism to integrate the material and provide cross-links across topics. In this paper, we present the Curriculum KG Ontology, which we use as a framework for the dense interlinking of educational materials, by first starting with organizational and broad pe…

A Unified Ontology for Scalable Knowledge Graph-Driven Operational Data Analytics in High-Performance Computing Systems
Junaid Ahmed Khan, Andrea Bartolini
https://arxiv.org/abs/2507.06107

A Unified Ontology for Scalable Knowledge Graph-Driven Operational Data Analytics in High-Performance Computing Systems
Modern high-performance computing (HPC) systems generate massive volumes of heterogeneous telemetry data from millions of sensors monitoring compute, memory, power, cooling, and storage subsystems. As HPC infrastructures scale to support increasingly complex workloads-including generative AI-the need for efficient, reliable, and interoperable telemetry analysis becomes critical. Operational Data Analytics (ODA) has emerged to address these demands; however, the reliance on schema-less storage s…

OntoRAG: Enhancing Question-Answering through Automated Ontology Derivation from Unstructured Knowledge Bases
Yash Tiwari, Owais Ahmad Lone, Mayukha Pal
https://arxiv.org/abs/2506.00664

OntoRAG: Enhancing Question-Answering through Automated Ontology Derivation from Unstructured Knowledge Bases
Ontologies are pivotal for structuring knowledge bases to enhance question answering (QA) systems powered by Large Language Models (LLMs). However, traditional ontology creation relies on manual efforts by domain experts, a process that is time intensive, error prone, and impractical for large, dynamic knowledge domains. This paper introduces OntoRAG, an automated pipeline designed to derive ontologies from unstructured knowledge bases, with a focus on electrical relay documents. OntoRAG integr…

Machine Learning-Driven Enzyme Mining: Opportunities, Challenges, and Future Perspectives
Yanzi Zhang, Felix Moorhoff, Sizhe Qiu, Wenjuan Dong, David Medina-Ortiz, Jing Zhao, Mehdi D. Davari
https://arxiv.org/abs/2507.07666

Machine Learning-Driven Enzyme Mining: Opportunities, Challenges, and Future Perspectives
Enzyme mining is rapidly evolving as a data-driven strategy to identify biocatalysts with tailored functions from the vast landscape of uncharacterized proteins. The integration of machine learning into these workflows enables high-throughput prediction of enzyme functions, including Enzyme Commission numbers, Gene Ontology terms, substrate specificity, and key catalytic properties such as kinetic parameters, optimal temperature, pH, solubility, and thermophilicity. This review provides a syste…

Tomorrow, we will dive deeper into ontologies with OWL, the Web Ontology Language. However, I'm doing OWL-lectures now for almost 20 years - and OWL as well as the lecture haven't changed much. So, I'm afraid I'm going to surprise/dissapoint the students tomorrow, when I will switch off the presentation and start improvising a random OWL ontology with them on the blackboard ;-)
#ise2025

Vers un cadre ontologique pour la gestion des comp{\'e}tences : {\`a} des fins de formation, de recrutement, de m{\'e}tier, ou de recherches associ{\'e}es
Ngoc Luyen Le (Heudiasyc), Marie-H\'el\`ene Abel (Heudiasyc), Bertrand Laforge (LPNHE)
https://arxiv.org/abs/2507.05767…

Vers un cadre ontologique pour la gestion des comp{é}tences : {à} des fins de formation, de recrutement, de m{é}tier, ou de recherches associ{é}es
The rapid transformation of the labor market, driven by technological advancements and the digital economy, requires continuous competence development and constant adaptation. In this context, traditional competence management systems lack interoperability, adaptability, and semantic understanding, making it difficult to align individual competencies with labor market needs and training programs. This paper proposes an ontology-based framework for competence management, enabling a structured re…

Generating Reliable Adverse event Profiles for Health through Automated Integrated Data (GRAPH-AID): A Semi-Automated Ontology Building Approach
Srikar Reddy Gadusu, Larry Callahan, Samir Lababidi, Arunasri Nishtala, Sophia Healey, Hande McGinty
https://arxiv.org/abs/2506.20851

Generating Reliable Adverse event Profiles for Health through Automated Integrated Data (GRAPH-AID): A Semi-Automated Ontology Building Approach
As data and knowledge expand rapidly, adopting systematic methodologies for ontology generation has become crucial. With the daily increases in data volumes and frequent content changes, the demand for databases to store and retrieve information for the creation of knowledge graphs has become increasingly urgent. The previously established Knowledge Acquisition and Representation Methodology (KNARM) outlines a systematic approach to address these challenges and create knowledge graphs. However,…

A Domain Ontology for Modeling the Book of Purification in Islam
Hessa Alawwad
https://arxiv.org/abs/2505.18222 https://arxiv.org/pdf…

A Domain Ontology for Modeling the Book of Purification in Islam
This paper aims to address a gap in major Islamic topics by developing an ontology for the Book of Purification in Islam. Many authoritative Islamic texts begin with the Book of Purification, as it is essential for performing prayer (the second pillar of Islam after Shahadah, the profession of faith) and other religious duties such as Umrah and Hajj. The ontology development strategy followed six key steps: (1) domain identification, (2) knowledge acquisition, (3) conceptualization, (4) class…

Defining and classifying models of groups: The social ontology of higher-order networks
Jonathan St-Onge, Randall Harp, Giulio Burgio, Timothy M. Waring, Juniper Lovato, Laurent H\'ebert-Dufresne
https://arxiv.org/abs/2507.02758

Defining and classifying models of groups: The social ontology of higher-order networks
In complex systems research, the study of higher-order interactions has exploded in recent years. Researchers have formalized various types of group interactions, such as public goods games, biological contagion, and information broadcasting, showing how higher-order networks can capture group effects more directly than pairwise models. However, equating hyperedges-edges involving more than two agents-with groups can be misleading, as it obscures the polysemous nature of ``group interactions''.…

Retrieval-Augmented Generation of Ontologies from Relational Databases
Mojtaba Nayyeri, Athish A Yogi, Nadeen Fathallah, Ratan Bahadur Thapa, Hans-Michael Tautenhahn, Anton Schnurpel, Steffen Staab
https://arxiv.org/abs/2506.01232

Retrieval-Augmented Generation of Ontologies from Relational Databases
Transforming relational databases into knowledge graphs with enriched ontologies enhances semantic interoperability and unlocks advanced graph-based learning and reasoning over data. However, previous approaches either demand significant manual effort to derive an ontology from a database schema or produce only a basic ontology. We present RIGOR, Retrieval-augmented Iterative Generation of RDB Ontologies, an LLM-driven approach that turns relational schemas into rich OWL ontologies with minimal…

Today in the ISE 2025 lecture on OWL, the Web Ontology Language. Tired of using slide presentations (at temperatures like today and giving the same presentation all over again), I spontaneously decided to design arbitrary OWL ontologies together with the students on the good old blackboard ;-)
#wayback #lecture

Patient Journey Ontology: Representing Medical Encounters for Enhanced Patient-Centric Applications
Hassan S. Al Khatib, Subash Neupane, Sudip Mittal, Shahram Rahimi, Nina Marhamati, Sean Bozorgzad
https://arxiv.org/abs/2506.18772

Patient Journey Ontology: Representing Medical Encounters for Enhanced Patient-Centric Applications
The healthcare industry is moving towards a patient-centric paradigm that requires advanced methods for managing and representing patient data. This paper presents a Patient Journey Ontology (PJO), a framework that aims to capture the entirety of a patient's healthcare encounters. Utilizing ontologies, the PJO integrates different patient data sources like medical histories, diagnoses, treatment pathways, and outcomes; it enables semantic interoperability and enhances clinical reasoning. By cap…

Energy as a Primitive Ontology for the Physical World
J. E. Horvath, B. B. Martins
https://arxiv.org/abs/2506.12692 https://arxiv.org…

Energy as a Primitive Ontology for the Physical World
We reanalyze from a modern perspective the bold idea of G. Helm, W. Ostwald, P. Duhem and others that energy is the fundamental entity composing the physical world. We start from a broad perspective reminding the search for a fundamental ``substance'' (perhaps better referred to as ous\'ıa, the original Greek word) from the pre-Socratics to the important debate between Ostwald and Boltzmann about the energy vs. atoms at the end of the 19th century. While atoms were eventually accepted (even by…

Navigating the growing field of research on AI for software testing -- the taxonomy for AI-augmented software testing and an ontology-driven literature survey
Ina K. Schieferdecker
https://arxiv.org/abs/2506.14640

Navigating the growing field of research on AI for software testing -- the taxonomy for AI-augmented software testing and an ontology-driven literature survey
In industry, software testing is the primary method to verify and validate the functionality, performance, security, usability, and so on, of software-based systems. Test automation has gained increasing attention in industry over the last decade, following decades of intense research into test automation and model-based testing. However, designing, developing, maintaining and evolving test automation is a considerable effort. Meanwhile, AI's breakthroughs in many engineering fields are opening…

Self-consciousness and personal identity in quantum panprotopsychism
Rodolfo Gambini, Jorge Pullin
https://arxiv.org/abs/2505.11530 https://

Self-consciousness and personal identity in quantum panprotopsychism
In previous papers, we demonstrated that an ontology of quantum mechanics, described in terms of states and events with internal phenomenal aspects (a form of panprotopsychism), is well suited to explain consciousness. We showed that the combination problems of qualities, structures and subjects in panpsychism and panprotopsychism stem from implicit hypotheses based on classical physics regarding supervenience, which are not applicable at the quantum level. Within this view, consciousness arise…

Replaced article(s) found for q-bio.OT. https://arxiv.org/list/q-bio.OT/new
[1/1]:
The Cell Ontology in the age of single-cell omics
https://