Ontologies
Peer Review as Structured Commentary: Immutable Identity, Public Dialogue, and Reproducible Scholarship
This paper reconceptualises peer review as structured public commentary. Traditional academic validation is hindered by anonymity, latency, and gatekeeping. We propose a transparent, identity-linked, and reproducible system of scholarly evaluation anchored in open commentary. Leveraging blockchain for immutable audit trails and AI for iterative synthesis, we design a framework that incentivises intellectual contribution, captures epistemic evolution, and enables traceable reputational dynamics. This model empowers fields from computational science to the humanities, reframing academic knowledge as a living process rather than a static credential.
Generating Reliable Adverse event Profiles for Health through Automated Integrated Data (GRAPH-AID): A Semi-Automated Ontology Building Approach
Gadusu, Srikar Reddy, Callahan, Larry, Lababidi, Samir, Nishtala, Arunasri, Healey, Sophia, McGinty, Hande
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, following this methodology highlights the existing challenge of seamlessly integrating Neo4j databases with the Web Ontology Language (OWL). Previous attempts to integrate data from Neo4j into an ontology have been discussed, but these approaches often require an understanding of description logics (DL) syntax, which may not be familiar to many users. Thus, a more accessible method is necessary to bridge this gap. This paper presents a user-friendly approach that utilizes Python and its rdflib library to support ontology development. We showcase our novel approach through a Neo4j database we created by integrating data from the Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) database. Using this dataset, we developed a Python script that automatically generates the required classes and their axioms, facilitating a smoother integration process. This approach offers a practical solution to the challenges of ontology generation in the context of rapidly growing adverse drug event datasets, supporting improved drug safety monitoring and public health decision-making.
Irec: A Metacognitive Scaffolding for Self-Regulated Learning through Just-in-Time Insight Recall: A Conceptual Framework and System Prototype
The core challenge in learning has shifted from knowledge acquisition to effective Self-Regulated Learning (SRL): planning, monitoring, and reflecting on one's learning. Existing digital tools, however, inadequately support metacognitive reflection. Spaced Repetition Systems (SRS) use de-contextualized review, overlooking the role of context, while Personal Knowledge Management (PKM) tools require high manual maintenance. To address these challenges, this paper introduces "Insight Recall," a novel paradigm that conceptualizes the context-triggered retrieval of personal past insights as a metacognitive scaffold to promote SRL. We formalize this paradigm using the Just-in-Time Adaptive Intervention (JITAI) framework and implement a prototype system, Irec, to demonstrate its feasibility. At its core, Irec uses a dynamic knowledge graph of the user's learning history. When a user faces a new problem, a hybrid retrieval engine recalls relevant personal "insights." Subsequently, a large language model (LLM) performs a deep similarity assessment to filter and present the most relevant scaffold in a just-in-time manner. To reduce cognitive load, Irec features a human-in-the-loop pipeline for LLM-based knowledge graph construction. We also propose an optional "Guided Inquiry" module, where users can engage in a Socratic dialogue with an expert LLM, using the current problem and recalled insights as context. The contribution of this paper is a solid theoretical framework and a usable system platform for designing next-generation intelligent learning systems that enhance metacognition and self-regulation.
medicX-KG: A Knowledge Graph for Pharmacists' Drug Information Needs
Farrugia, Lizzy, Azzopardi, Lilian M., Debattista, Jeremy, Abela, Charlie
The role of pharmacists is evolving from medicine dispensing to delivering comprehensive pharmaceutical services within multidisciplinary healthcare teams. Central to this shift is access to accurate, up-to-date medicinal product information supported by robust data integration. Leveraging artificial intelligence and semantic technologies, Knowledge Graphs (KGs) uncover hidden relationships and enable data-driven decision-making. This paper presents medicX-KG, a pharmacist-oriented knowledge graph supporting clinical and regulatory decisions. It forms the semantic layer of the broader medicX platform, powering predictive and explainable pharmacy services. medicX-KG integrates data from three sources, including, the British National Formulary (BNF), DrugBank, and the Malta Medicines Authority (MMA) that addresses Malta's regulatory landscape and combines European Medicines Agency alignment with partial UK supply dependence. The KG tackles the absence of a unified national drug repository, reducing pharmacists' reliance on fragmented sources. Its design was informed by interviews with practicing pharmacists to ensure real-world applicability. We detail the KG's construction, including data extraction, ontology design, and semantic mapping. Evaluation demonstrates that medicX-KG effectively supports queries about drug availability, interactions, adverse reactions, and therapeutic classes. Limitations, including missing detailed dosage encoding and real-time updates, are discussed alongside directions for future enhancements.
A GenAI System for Improved FAIR Independent Biological Database Integration
Sakib, Syed N., Naha, Kallol, Rubaiat, Sajratul Y., Jamil, Hasan M.
Life sciences research increasingly requires identifying, accessing, and effectively processing data from an ever-evolving array of information sources on the Linked Open Data (LOD) network. This dynamic landscape places a significant burden on researchers, as the quality of query responses depends heavily on the selection and semantic integration of data sources --processes that are often labor-intensive, error-prone, and costly. While the adoption of FAIR (Findable, Accessible, Interoperable, and Reusable) data principles has aimed to address these challenges, barriers to efficient and accurate scientific data processing persist. In this paper, we introduce FAIRBridge, an experimental natural language-based query processing system designed to empower scientists to discover, access, and query biological databases, even when they are not FAIR-compliant. FAIRBridge harnesses the capabilities of AI to interpret query intents, map them to relevant databases described in scientific literature, and generate executable queries via intelligent resource access plans. The system also includes robust tools for mitigating low-quality query processing, ensuring high fidelity and responsiveness in the information delivered. FAIRBridge's autonomous query processing framework enables users to explore alternative data sources, make informed choices at every step, and leverage community-driven crowd curation when needed. By providing a user-friendly, automated hypothesis-testing platform in natural English, FAIRBridge significantly enhances the integration and processing of scientific data, offering researchers a powerful new tool for advancing their inquiries.
Consistency Verification in Ontology-Based Process Models with Parameter Interdependencies
Jeleniewski, Tom, Nabizada, Hamied, Reif, Jonathan, Gehlhoff, Felix, Fay, Alexander
--The formalization of process knowledge using ontologies enables consistent modeling of parameter interdependencies in manufacturing. These interdependencies are typically represented as mathematical expressions that define relations between process parameters, supporting tasks such as calculation, validation, and simulation. T o support cross-context application and knowledge reuse, such expressions are often defined in a generic form and applied across multiple process contexts. This highlights the necessity of a consistent and semantically coherent model to ensure the correctness of data retrieval and interpretation. Consequently, dedicated mechanisms are required to address key challenges such as selecting context-relevant data, ensuring unit compatibility between variables and data elements, and verifying the completeness of input data required for evaluating mathematical expressions. This paper presents a set of verification mechanisms for a previously developed ontology-based process model that integrates standardized process semantics, data element definitions, and formal mathematical constructs. The approach includes (i) SPARQL-based filtering to retrieve process-relevant data, (ii) a unit consistency check based on expected-unit annotations and semantic classification, and (iii) a data completeness check to validate the evaluabil-ity of interdependencies. The applicability of the approach is demonstrated with a use case from Resin Transfer Molding (RTM), supporting the development of machine-interpretable and verifiable engineering models.
Bayesian Epistemology with Weighted Authority: A Formal Architecture for Truth-Promoting Autonomous Scientific Reasoning
The crisis of epistemic overload in modern scientific inquiry has exposed a critical deficiency in how truth claims are assessed, validated, and integrated across time and domain. The exponential growth in peer-reviewed publications, accompanied by inconsistent replication rates, entrenched citation biases, and the sociological entanglements of scientific authorship, has rendered traditional mechanisms of epistemic filtering increasingly obsolete. Simultaneously, artificial intelligence--while having demonstrated capacity in data correlation and language generation--remains fundamentally ill-equipped to perform rigorous epistemic reasoning. This gap is not merely technical but conceptual: current AI systems lack any principled framework for evaluating the truth-promoting value of claims, discerning authoritative sources, or understanding belief as a structured probabilistic relation between agents, claims, and contexts. The present work introduces a formal architecture--Bayesian Epistemology with Weighted Authority (BEW A)--which systematically encodes the logic of belief formation, update, and decay, guided by the core axioms of Bayesian rationality, tempered by structural mechanisms for authority weighting, replication scoring, and temporal reassessment.
Enhancing Object Search in Indoor Spaces via Personalized Object-factored Ontologies
Chikhalikar, Akash, Ravankar, Ankit A., Luces, Jose Victorio Salazar, Hirata, Yasuhisa
Personalization is critical for the advancement of service robots. Robots need to develop tailored understandings of the environments they are put in. Moreover, they need to be aware of changes in the environment to facilitate long-term deployment. Long-term understanding as well as personalization is necessary to execute complex tasks like prepare dinner table or tidy my room. A precursor to such tasks is that of Object Search. Consequently, this paper focuses on locating and searching multiple objects in indoor environments. In this paper, we propose two crucial novelties. Firstly, we propose a novel framework that can enable robots to deduce Personalized Ontologies of indoor environments. Our framework consists of a personalization schema that enables the robot to tune its understanding of ontologies. Secondly, we propose an Adaptive Inferencing strategy. We integrate Dynamic Belief Updates into our approach which improves performance in multi-object search tasks. The cumulative effect of personalization and adaptive inferencing is an improved capability in long-term object search. This framework is implemented on top of a multi-layered semantic map. We conduct experiments in real environments and compare our results against various state-of-the-art (SOTA) methods to demonstrate the effectiveness of our approach. Additionally, we show that personalization can act as a catalyst to enhance the performance of SOTAs. Video Link: https://bit.ly/3WHk9i9
Quantum AGI: Ontological Foundations
Perrier, Elija, Bennett, Michael Timothy
We examine the implications of quantum foundations for AGI, focusing on how seminal results such as Bell's theorems (non-locality), the Kochen-Specker theorem (contextuality) and no-cloning theorem problematise practical implementation of AGI in quantum settings. We introduce a novel information-theoretic taxonomy distinguishing between classical AGI and quantum AGI and show how quantum mechanics affects fundamental features of agency. We show how quantum ontology may change AGI capabilities, both via affording computational advantages and via imposing novel constraints.
On Immutable Memory Systems for Artificial Agents: A Blockchain-Indexed Automata-Theoretic Framework Using ECDH-Keyed Merkle Chains
This paper presents a formalised architecture for synthetic agents designed to retain immutable memory, verifiable reasoning, and constrained epistemic growth. Traditional AI systems rely on mutable, opaque statistical models prone to epistemic drift and historical revisionism. In contrast, we introduce the concept of the Merkle Automaton, a cryptographically anchored, deterministic computational framework that integrates formal automata theory with blockchain-based commitments. Each agent transition, memory fragment, and reasoning step is committed within a Merkle structure rooted on-chain, rendering it non-repudiable and auditably permanent. To ensure selective access and confidentiality, we derive symmetric encryption keys from ECDH exchanges contextualised by hierarchical privilege lattices. This enforces cryptographic access control over append-only DAG-structured knowledge graphs. Reasoning is constrained by formal logic systems and verified through deterministic traversal of policy-encoded structures. Updates are non-destructive and historied, preserving epistemic lineage without catastrophic forgetting. Zero-knowledge proofs facilitate verifiable, privacy-preserving inclusion attestations. Collectively, this architecture reframes memory not as a cache but as a ledger - one whose contents are enforced by protocol, bound by cryptography, and constrained by formal logic. The result is not an intelligent agent that mimics thought, but an epistemic entity whose outputs are provably derived, temporally anchored, and impervious to post hoc revision. This design lays foundational groundwork for legal, economic, and high-assurance computational systems that require provable memory, unforgeable provenance, and structural truth.