Knowledge Representation

This paper asks how explicit representations can support reusable cognitive schemas in knowledge-based problem solving. We develop a structural framework in which schemas are organized by the information and relations required for their use, rather than introduced as unrelated primitives. The framework also distinguishes context-dependent relations from more stable structures that can be reused across different representations. Tasks are described through the information available, the unknowns to be determined, and the constraints that admissible solutions must satisfy. This makes it possible to separate limitations of the representation from limitations of the solving procedure. In particular, we distinguish inconsistency, underdetermination, and contextual insufficiency, where the current representation lacks distinctions or relations required by the external task meaning. We also show formally when a reduction of representation preserves the task-relevant solution structure. The resulting task--schema interface offers a structured way to describe representational conditions relevant to problem solving. It supports the reuse and stabilization of derived knowledge while remaining independent of the particular mechanism used to generate candidate solutions. This may provide a useful component for future solver architectures that combine structured knowledge, verification, and learned proposal mechanisms.

Scientific language models often access literature through untyped text chunks, which fragment the functional and evidential structure required for mechanism-rich questions. We introduce an evidence-grounded mechanism knowledge substrate that organizes scientific literature into provenance-linked evidence units, role-typed entities, and directed mechanism paths. We instantiate it as MS$^3$, a Material-Sensor-Signal-System schema for conductive-fiber flexible sensors, over 13,689 papers, 131,083 evidence items, and 26,648 mechanism objects. On in-domain and coverage-shift question-answering benchmarks, we compare closed-book generation, Web search, Raw-PDF RAG, and MS$^3$ retrieval across ten language models. MS$^3$ improves macro-averaged scientific correctness. It also improves citation entailment and answer completeness. These results support mechanism substrates as a reliable representation layer for scientific language models and motivate a source-repair workflow in which insufficient MS$^3$ evidence triggers targeted retrieval from its linked papers rather than assuming that a user has already supplied the correct PDFs.

Ontology documentation, visualization, and validation are usually carried out with separate tools. This split workflow slows down development and makes knowledge transfer harder. We present OntoInk, an open-source MkDocs plugin that brings these activities together. Within a single documentation-as-code pipeline, OntoInk renders interactive ontology diagrams, validates instance data against SHACL shapes, runs OWL,DL reasoning, and supports inline Turtle editing. General-purpose diagram plugins for MkDocs cannot parse RDF, dereference IRIs, overlay SHACL constraints, or run OWL reasoning. Compared with standalone ontology visualization tools, OntoInk embeds interactive and editable diagrams directly into documentation pages. A live demo and source code are available at https://ise-fizkarlsruhe.github.io/ontoink/.

This paper presents the European Crisis Management Ontology (ECMO), a modular OWL-based ontology intended as a cross-sectoral reference for disaster risk reduction and response. ECMO is designed to be organised as a network of ontological modules. Among the modules, ECMO-CORE captures fundamental crisis management concepts such as hazard, event, exposure, impact, and response measure and uses ontology design patterns and the OWL2 punning technique to resolve ambiguities between hazard types and event manifestations. In addition, domain-specific modules are defined as in the case of the public health module aligned with SNOMED CT and ICD-11. To demonstrate the resource's utility, we used ECMO to represent the data of the Epidemic Intelligence from Open Sources system of the Joint Research Centre to generate an end-to-end pipeline that populates an ECMO-compliant knowledge graph from unstructured epidemiological news. Initial results demonstrate that ECMO provides the formal guardrails necessary for consistent and unified knowledge representation and integration. The ontology is publicly available at https://doi.org/10.5281/zenodo.20070268 and is released under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.

Enterprise information is represented through artifacts shaped by applications, projects, technologies, organizational boundaries, and local requirements. These structures accumulate over time, creating representational complexity that must be maintained by the enterprise and interpreted by information consumers and AI systems. This paper introduces Enterprise Representation Simplification (ERS) as reducing unnecessary representational complexity while preserving required information within a defined scope, and Enterprise Representation Complexity (ERC), a representation-neutral model for comparing complexity across representation states. ERC characterizes representational extent through four dimensions: Representation Objects, Interactions, Behaviors, and Supporting Sources. Objects, Interactions, and Behaviors form dependent categories, while Supporting Sources characterize representation exposure. ERC is defined at representation and task levels, enabling comparison and distinguishing architectural simplification from retrieval optimization. The paper develops two consequences of ERS. First, representational structures create lifecycle obligations for maintenance, governance, dependencies, change, enhancement, and operation. An economic model distinguishes recurring global representation cost, recurring task-level cost, and one-time transformation cost, enabling evaluation over a defined time horizon. Second, reductions in task-level ERC reduce the representational extent an AI system must identify, relate, and interpret. Text-to-SQL research provides evidence that reduced schema and reasoning complexity can improve reasoning accuracy. ERC is not a universal complexity, performance, or cost metric. It provides measurable architectural variables for comparing representational alternatives, transformation effects, economic outcomes, and AI reasoning performance.

Transforming raw data into queryable knowledge requires both early extraction of reusable information and explicit types, relations, and applicability conditions for particular tasks. If indexing selects content too early around a single business schema, later tasks may be unable to use information that was omitted. If the index retains only open-ended text, however, rule-based reasoning lacks checkable premises. We propose 5W1H+Which, a semantic indexing design that separates content extraction from ontology binding. The 5W1H questions organize source-grounded content units; Which points to versioned ontology elements and records mapping relations, scope, and validation status. Time, location, system environment, and participant roles are not merely retrieval labels: together, they constrain the contexts in which facts, bindings, and rules apply. Unbound content remains searchable, while bound content enters a formal reasoning path only after premise checks. The method further distinguishes business valid time, system knowledge time, and operational traces, and uses dependency records to support binding revalidation and the maintenance of derived conclusions. A worked example of migration from an on-premises server to a cloud environment illustrates the different treatment of world-state changes, ontology-version changes, and changes in rule applicability. We formulate three groups of falsifiable hypotheses concerning cross-task evidence coverage, control of contextual misuse, and incremental update cost. The planned evaluation includes a strong typed fact-graph baseline with the same evidence, temporal information, and budget, to test whether benefits arise from 5W1H organization, deferred binding, or additional information and engineering effort. The contribution is a testable indexing mechanism, not a claim to a new universal ontology or a demonstrated performance advantage.

Agentic science envisions many autonomous agents investigating concurrently while building on a shared, evolving body of scientific knowledge. This requires a knowledge foundation that supports high-concurrency access, preserves traceable and reusable reasoning, and grows incrementally. We propose the Large Knowledge Model (LKM), a growing, agent-native knowledge foundation that provides a general representation of scientific knowledge across disciplines. LKM organizes the scientific literature into reasoning graphs, with claims as the core nodes and associated reasoning chains that make explicit how premises and evidence support conclusions. These source-grounded objects are persistent and addressable; cross-paper links organize them into aligned question, workflow, and evidence views. Newly extracted papers extend the foundation incrementally while preserving existing object identities. Building on this foundation, we develop an agent-native, reasoning-aware scientific retrieval system that retrieves claims together with their reasoning chains and sources, enabling agents to inspect and reuse the evidence underlying scientific conclusions. Across benchmarks, agents using LKM retrieve more evidence, cite more faithfully, and answer scientific questions more accurately: LKM nearly doubles the known supporting and contradicting evidence retrieved on SciFact-Open (818 versus 443 claim-paper pairs), reasoning graphs raise citation F1 on ScholarQABench by more than 5 points over the same retrieved papers, and LKM retrieval improves a fixed answering model by 9.3, 4.2, and 14.7 points over no retrieval on ChemBench, PubMedQA, and SciBench. LKM lays the foundation for a scientific ecosystem in which AI scientists not only recall accumulated knowledge but also extend it, returning new questions, workflows, and evidence to a memory that every subsequent investigation can build on.

Scientific papers keep much of their quantitative content in tables and supplementary files, where a number means something only through its header, caption, unit, analytical method, and the conventions of its field. Recovering the rows and columns of a table is therefore not the same as recovering the scientific fact it reports. Most semantic table-interpretation methods assume that a clean table is already available and subsequently map its cells or columns to ontology terms, whereas most publication-level extraction systems are designed for a single domain. We study a middle path: a shared process that reads a paper and its supplementary files, gathers evidence from several parsers and a language model, and reconciles that evidence, while a bounded human-authored task module for each task supplies the domain meaning. The module lists the canonical names the graph may use, the surface forms that map to them, a small set of derivation rules and validity constraints, an identity key, and the bindings used to write RDF. It defines what a task is allowed to emit; it does not try to list every convention of a field. We build four such modules (for drug-discovery chemistry, materials science, machine learning, and mineral geochemistry) in the ArticleMiner framework, and evaluate them on 163 papers, including a new geochemistry benchmark with expert-curated ground truth. In comparisons against a same-LLM few-shot baseline, the point estimates favor ArticleMiner on all four tasks, with uncertainty on the two smaller benchmarks. The geochemistry comparison also includes access to supplementary files, so its improvement cannot be attributed to domain guidance alone.

Large language models are increasingly deployed as course-specific tutors, but their usefulness depends on grounding in vetted instructional materials that are often revised mid-semester. Our prior work built a multimodal retrieval-augmented generation (RAG) system over an authentic machine learning course corpus (Foundations of Machine Learning) and found that retrieval improved contextual grounding, but that fixed retrieval strategies were suboptimal. That motivates a different question: whether how a corpus is structured at ingest time matters more than how much is retrieved at query time. We present a controlled head-to-head comparison of two knowledge representations over an identical classroom corpus: (A) vector RAG, replicating the best-performing configuration from our prior study, and (B) an LLM-compiled wiki (Karpathy framework), in which the corpus is synthesized at ingest into linked concept pages with explicit cross-references and citations back to source materials. We evaluate 59 questions spanning single-fact recall, cross-unit concept linking, synthesis and explanation, and currency after a syllabus revision, scored by an LLM judge against a human-authored rubric. Both representations answered single-fact questions about equally well (9.33 vs. 9.96 of 10), but diverged sharply on questions requiring links across course units. The compiled wiki remained accurate and grounded (9.93; 100% grounded in cited sources), while retrieval scored lower and was markedly less grounded (8.14; 64%). The wiki's citations let students and instructors trace any claim back to the lecture that introduced it, adding a layer of dynamic retrieval that machine learning courses require. While further testing is needed, instructors using AI to support learning in ML courses should consider wiki-based structure for its potential to support foundational elements of best practice.

The conventional testing process quickly fails when applied to ML-based systems such as obstacle detection in vehicles: if an obstacle is not detected in a test, classical bug fixing is impossible and an AI system will always retain shortcomings. Test results can therefore only be interpreted statistically, which in turn requires test sets that are not only complete with respect to the operational design domain (ODD) of the system, but also representative of it. To this end, we introduce probabilistically extended ontologies (PEONs): ontologies describing the ODD, augmented with a probability distribution over the partitioning they induce. Instead of unmaintainable conditional probability tables, only marginal distributions and functionally described dependencies need to be specified; algorithms based on couplings and optimal transport complete this specification to a Bayesian network. From a PEON we derive the sampling of representative test cases, rigorous end-of-test criteria for given quality targets and significance levels, and methods for re-evaluating existing test results and for assessing the balance of training data. We demonstrate the practical modelling of a complex ODD using the example of automatic train operation.

In various data models, the classical triple is a typical semantic data model. However, due to the design of the triple as a simple structure for representing positive assertions, it cannot sufficiently express different forms of negation present in the triple and its elements. This paper conceptually proposes that there are three distinct forms of negation within triples and their elements: contradictory negation, opposite negation and intermediary negation. Based on the the set SCOI and the logic LCOI+PLCOI with three kinds of negation, we propose an extension of triple that can distinguish and express these three different negations in the triple and its elements, called the TCOI triple with contradictory negation, opposite negation and intermediary negation. The TCOI triple is a semantic and structural extension of the classical triple. While retaining the ability to express positive assertions, it systematically introduces the three semantic dimensions of three negations, allowing these negations to independently act on the elements of the triple and on the whole triple. This significantly enhances the triple model capability to represent and reasoning about complex negative information. This paper also explores the expressive power and reasoning of the TCOI triple, as well as the application of TCOI triple implication reasoning in counterfactuals and counterfactual reasoning. We propose a truth-value (continuous value) algorithm for TCOI triple implication reasoning and perform its calculation through an example of the counterfactuals and counterfactual reasoning.

Humans can learn and generalize novel concepts from sparse data because they express knowledge in rich structural formats. In this paper, we propose that programs are a strong candidate for universal representation of concepts. We review computational models of concept learning that use programs as their concept representation and evaluate their contribution toward a universal representational language.

Knowledge graphs describe reality in crisp assertions, while the systems now consuming them, foundation models and autonomous agents, reason natively in probabilities. We argue that this mismatch is why the integration of language models and knowledge graphs remains a data-feeding pipeline rather than a unified reasoning architecture. We envision Semantic Bayesian World Models (SBWMs): a Web that describes the world not as a database of facts but as a shared, evolving fabric of beliefs over knowledge graphs, where ontological axioms constrain priors, observations update beliefs by Bayesian conditioning, and actions intervene upon the world. We work through what an agent gains from such a model: a home-security agent deciding whether the figure at the gate is a courier or a burglar, an actuarial estimate aggregated by entailment rather than by string frequency, a planning task that language models reliably fail, and the estimation of quantities that no document has ever stated. We then set out what the community must build to make them possible: belief annotation over RDF~1.2, probabilistic entailment regimes, semantic calibration layers, and protocols by which agents that have never met can exchange, and disagree over, calibrated beliefs.

We present the zbMATH Open Knowledge Graph, a large-scale RDF knowledge graph (KG) covering more than 250 years of mathematical scholarship. Unlike existing scholarly knowledge graphs that primarily capture bibliographic metadata and citation structures, the zbMATH Open KG integrates expert-curated semantic content, including reviews, keywords, subject classifications, software references, and disambiguated authorship. This combination of domain-specific representation of mathematical knowledge and extensive temporal coverage supports analyses that require fine-grained exploration of mathematical concepts, research fields, and scholarly relationships over time. The resulting graph comprises 34 million entities and 168 million RDF triples represented using established Semantic Web vocabularies, supporting interoperability and FAIR data principles. We further demonstrate its capabilities through query-driven historically grounded scholarly exploration use cases, illustrating how the knowledge graph can surface relationships and patterns that may be difficult to identify from bibliographic and citation information alone. The zbMATH Open KG provides an open semantic infrastructure for studying the development of mathematical knowledge and tracing scholarly connections across centuries of scholarship.

Introduction: NICE guidelines provide evidence-based recommendations for clinical care but remain largely in unstructured natural language. Existing approaches to converting them into computable representations often focus on individual diseases, require substantial manual encoding, and do not scale. Large language models (LLMs) may enable much of this translation to be automated. Methods: We present an end-to-end approach that converts textual clinical guidelines into executable models capable of generating explainable, patient-specific recommendations. A stepwise LLM-based transformation with in-context examples produces human-inspectable intermediate artifacts. We apply the approach to NICE pancreatic and lung cancer guidelines, use expert review to assess rule alignment, and evaluate the executable pancreatic cancer model on 20 patient vignettes. Results: Expert review showed strong alignment between the source guidelines and generated executable models. Most discrepancies were partial omissions rather than incorrect logic, while hallucinated or fundamentally incorrect rules were rare. On the patient vignettes, the executable model achieved an F1 score of 82.5%. Conclusion: LLMs can transform natural-language NICE guidelines into interpretable, executable models that preserve guideline structure, support transparent inspection and modification, and generate patient-specific recommendations. These findings demonstrate the feasibility of scalable automated generation of computable clinical guidelines.

Motivation: LinkML is a suitable language for the representation of the structural and content constraints of different kinds of biomedical data. Even if it is a quite recent proposal, it has been applied in several biomedical contexts. Developing and maintaining LinkML schemas presents several challenges, particularly for novice curators. Non-expert bio-curators may struggle with LinkML syntax and best practices, requiring significant time and effort to develop well-structured schemas. Results: In this paper we propose SchemaLink, a web-based environment for the graphical construction and enhancement of LinkML schemas that address the following requirements: $(i)$ introduce a graphical language for the specification of LinkML schemas, $(ii)$ make uniform the specification of schemas in similar contexts, $(iii)$ simplify the design and curation processes by exploiting a RAG-based approach to assist curators in creating new schemas from scratch and editing already developed ones. Several experimental analyses show the quality of the produced LinkML schemas through the AI-based editing facilities. Availability and Implementation: SchemaLink is available online at: https://SchemaLink.biodata.di.unimi.it. SchemaLink code and testing data are available as open-source on GitHub at: https://github.com/AnacletoLAB/{schemalink-webapp,schemalink-api}.

The increasing specialization of scientific research challenges existing classification systems, which provide effective representations of broad disciplines and research topics but often fail to capture the fine-grained conceptual structure of contemporary science. Author keywords offer greater specificity, but their fragmentation, redundancy, and terminological variability limit their use as stable units of knowledge organization. We introduce SCALE (Scientific Concept Aggregation via LLMs and Embeddings), a framework that extends the OpenAlex taxonomy with a new level of scientific Concepts below Topics. Rather than treating keywords as isolated descriptors, SCALE organizes semantically related terms into coherent and interpretable conceptual units and integrates them within the existing disciplinary hierarchy. The framework combines scientific text embeddings, large language models, and graph-based community detection to construct this additional layer at scale. The resulting taxonomy enables scientific literature to be read through an intermediate conceptual level between broad research topics and individual documents. This perspective provides a more detailed representation of how scientific knowledge is structured, specialized, and connected across disciplines. By transforming heterogeneous author terminology into reusable hierarchical units, SCALE offers a foundation for fine-grained scholarly classification, scientometric analysis, research monitoring, and future ontology development.

The emergence of the ISO standard GQL introduces a powerful query language extending first-order logic with controlled recursion, raising the question of its applicability to evaluation of ontology-mediated queries (OMQs). We focus on OMQs consisting of atomic queries over ontologies expressed in Horn-ALCHI, an expressive Description Logic that is not, in general, first-order rewritable. To address this, we introduce DL automata, a novel formalism that captures the semantics of such OMQs via runs over fact sets. We then identify a large class of DL automata that can be rewritten into unions of conjunctive two-way regular path queries (UC2RPQs), a central fragment of GQL. Our class of automata relies on a stratification of their states, ruling out specific forms of cyclic dependencies known to raise the complexity. This yields a broad class of Horn-ALCHI OMQs that are GQL-rewritable.

The "decompose-then-verify" paradigm for LLM factuality evaluation faces a fundamental trade-off: atomic facts, i.e., one sentence conveying one unit of information, often omit essential context, while broader statements lack the granularity needed for precise assessment. To address this, we introduce TriQua, a framework that flexibly models facts based on their complexity. Simple claims are extracted as standard triples, while complex claims are represented as hyperrelational facts by attaching auxiliary contextual qualifiers. This adaptive structure preserves the necessary context for accurate retrieval and verification without sacrificing atomicity. Furthermore, TriQua's verification process directly annotates concrete errors within specific triples and qualifiers, providing fine-grained explainability for error detection. Alongside the framework, we propose TriQuaScore to quantify the factuality of these structured fact units. Empirical evaluations show that TriQuaScore strongly aligns with human annotated factuality scores, TriQua achieves robust decomposition quality, and outperforms existing decomposition-based frameworks in evidence-based fact verification.

Subtask labels decompose a long-horizon manipulation demonstration into shorter semantic segments for policy training and evaluation. Natural language descriptions are easy to read, but their linguistic variability makes automatic verification difficult. Rigid template formats, such as BEHAVIOR-1K's skill_annotation, are linguistically over-segmented, hindering both readability and annotation consistency. We propose the Structured Subtask Chain (SSC), a state-transition representation that bridges these extremes. A demonstration is a sequence of Structured Subtask Template (SST) entries. Each SST stores core action components (subject, predicate, object), flexible conditions (adverbial modifiers such as spatial or instrumental phrases), a base-motion field separate from arm actions, and an after-state scene graph. Built on this format, SSC supports three vision-language assisted functions: rendering SSTs as natural language, checking the assembled chain against four state-transition rules, and completing underspecified fields through a query resolution cascade. We instantiate the pipeline on BEHAVIOR-1K (50 tasks, 3 episodes per task, 2,357 annotated action cells) for logic verification and content completion, evaluating 13 selected state-of-the-art VL models as candidate verifiers and reporting labelling anomalies.

The subject matter of this paper is twofold. One is to review the theoretical foundation of a specific type of Semantic Networks (SNs) representing textual non-propositional knowledge. The other involves proposing a framework (ClueNetwork) for ranking candidate SNs generated through various Semantic Network Construction (SNC) processes for the type. In the first fold, it is clarified that the type serves as clues, not surrogates, of reality, making gold standards elusive. Then, it is discussed why this type nevertheless holds scientific legitimacy in terms of abduction. Grounded in this legitimacy, the three main stages of SNC, comprising Automatic Keyphrase Extraction (AKE), Edge Weighting (EW), and Community Detection (CD), are reviewed alongside their objectives and operations. In the second fold, evaluation criteria (comprising two established and one reformulated) for achieving the objectives are first defined and justified, followed by illustrative experiments based on the criteria. Thereafter, SNC is reformulated as a Process Optimization Problem (POP), and its global objective function that integrates the local criteria is defined and justified. Based on these, ClueNetwork is ultimately proposed.

Meta-analysis synthesis highlights a fundamental challenge in knowledge-based scientific analysis: structured evidence does not by itself represent the analytical knowledge required for executable computation. Decisions about evidence assignment, analytical contrasts, outcome and time-point alignment, effect-size formulation, and methodological admissibility must be explicit before statistical execution. Existing automated approaches often embed these decisions in model outputs, generated code, or workflow traces rather than representing them as independently verifiable knowledge. We introduce the Executable Analytical Knowledge Representation (EAKR), a machine-actionable representation of the knowledge required to transform structured evidence into executable meta-analysis. An EAKR represents evidence, relations, numerical inputs, constraints, provenance, and unresolved issues. We operationalise EAKR in MetaSynDec, an agentic harness in which large language models propose structured updates and deterministic services govern schema- and contract-based validation and execution. Across 58 synthesis units, MetaSynDec constructed all EAKRs, with 57 proceeding to statistical execution. Of 56 units with sufficient information to define a reference analysis object, 38 (67.9%) achieved complete object fidelity and 42 (75.0%) exact evidence-set agreement, with a mean Jaccard similarity of 0.909. Generated and published confidence intervals overlapped in 54 of 55 units (98.2%). MetaSynDec outperformed direct LLM generation in reference synthesis-structure agreement (57/58 versus 23/58; p<0.001) and among 23 jointly completed units, exact reference-formulation agreement (23/23 versus 1/23; p<0.001). These findings provide feasibility evidence that EAKR supports formal validation, traceability, statistical execution, and improved methodological agreement relative to direct LLM generation.

On-policy self-distillation (OPSD) improves reasoning by using a privileged view of a model conditioned on reference solutions to supervise a student view that observes only the question. However, the teacher-provided token-level targets may depend on reference-specific information unavailable at inference time. We propose Problem-Space-Guided OPSD (PS-OPSD), which replaces the complete solution with trajectory-grounded guidance describing the initial state, goal conditions, constraints, and a selected state-transition path. The student rollout and OPSD objective remain unchanged. Across three mathematical reasoning benchmarks and model scales ranging from 1.7B to 8B, PS-OPSD achieves the highest aggregate question-only accuracy among the compared methods. Controlled experiments further indicate that guidance relevance and path coherence contribute to these gains, highlighting the representation of privileged information as an important design choice in OPSD.

Datalog rules are often used to define ontologies over Knowledge Graphs. Rule reasoners routinely optimise such ontologies by rewriting their rules into a form that can be evaluated more efficiently. These transformations preserve the entailed facts, but not the structure of the underlying derivations. A proof tree under the rewritten rules explains why a fact holds, but does not readily yield an explanation in terms of the original rules. We study the problem of constructing, from a proof of entailment under the rewritten rules, a proof under the original ones: we establish its computational complexity and identify two practically relevant languages for specifying proof transformations.

Organizations increasingly define operational metrics in structured, machine-readable formats to monitor systems, processes, and compliance. These metric definitions implicitly encode domain knowledge, such as referencing concepts, properties, and relationships, that often extends what is captured in formal ontologies. Yet the connection between operational metric catalogues and ontological knowledge remains manual, ad-hoc, and labor-intensive. We present COntExt, a framework for context-aware ontology extension that takes structured metric definitions as input and suggests how referenced concepts and properties should be integrated into an existing ontology, utilizing the context of these metrics. The framework defines the extension problem as three sub-tasks: parent class prediction, relation type prediction, and data property assignment. Across four cybersecurity ontologies, we evaluate different algorithms for each task. Our results show that metric-derived context improves the suggestions over ontology-context baselines for relation type prediction and data property assignment. Our work demonstrates that operational metric catalogues are a practical and underexploited source for ontology extension. This work enables organizations to maintain their ontologies at a significantly lower cost than manual engineering.

Combining RDF rule languages, such as N3 or SHACL Rules, with default negation is challenging. Existing methods to stratify negation often fail for RDF rules, since individual triples do not carry enough information to meaningfully restrict potential dependencies. Blank nodes in rule heads further complicate the matter, since the order of rule applications may determine whether new values are created, which in turn can change the applicability of rules with negation. To solve these open problems, we propose chain stratification as a robust new condition that guarantees a well-behaved semantics for RDF rules with negation, and existential rules in general. Our condition combines an elaborate analysis of potential multistep derivations with a mechanism for using integrity constraints to discard impossible cases. Applying rules in any order that respects chain stratification is guaranteed to derive an RDF graph that is unique, lean, and justified under the usual negation-as-failure semantics. To show the practicality, we also provide a prototype implementation.

Scientific processes are often described in heterogeneous article discourse, with details needed for comparison, reproducibility, reuse, and automation dispersed across prose, tables, figures, protocols, and supplementary files. We present the first release of SciSchema.org, a multidisciplinary collection of 16 expert-annotated schemas spanning Biology & Biotechnology, Materials & Chemistry, Imaging & Measurement, Physics, and Psychology. Each schema defines reusable fields for describing process instances, including inputs, outputs, materials, instruments or software, parameters, conditions, procedural steps, measurements, and provenance-related information. The schemas were created through a human-in-the-loop schema-mining workflow in which large language models generated candidate structures from process specifications, scientific articles, and expert feedback, followed by domain-expert construction of final master schemas. The dataset contains final schemas in JSON Schema and SHACL formats, intermediate model-generated schemas, expert-feedback records, source-paper metadata, community-development materials, and analysis scripts. Technical validation assessed schema structure, development provenance, expert review, and syntactic conformance. The collection supports structured annotation, metadata enrichment, scientific knowledge graphs, information extraction, semantic publishing, and cross-study comparison.

SHACL shapes enable data graph validation, making automatic shape learning essential for knowledge graph applications. We investigate the well-known fitting approach to this task: given sets P and N of positive and negative example nodes from an input graph, compute a shape expression C, possibly using shape names defined in a recursive shape catalogue, that validates at every node in P and none in N. We focus on the case where C is written in a core fragment of SHACL corresponding to the Description Logic ELI. For the catalogue, we consider the well-founded, stable, and supported semantics. We address fitting existence and most specific fitting computation, establish tight exponential-time upper bounds for both problems, and obtain polynomial bounds for relevant special cases.

We propose the Virtual Process Dossier (VPD), a Knowledge Graph-based data catalogue that also captures workflow provenance. We developed VPD for multi-stage manufacturing use-cases where downstream AI-based optimization tasks require to distinct between datasets generated during individual workflow steps. VPD provides these datasets in a FAIR manner and makes both prospective and retrospective workflow provenance explicit. Our contributions are: (1) the VPD ontology that serves as the catalogue's semantic core; (2) the VPD provenance framework that integrates ontology instantiation into the production environment; and (3) the VPD user interface that provides human-centered interaction with the VPD Knowledge Graph. The ontology and code are available at https://github.com/kubeluk/VirtualProcessDossier .

Ontology matching (OM) has traditionally been formulated as either equivalence discovery or subsumption matching. The existing OM systems identify only one type of semantic correspondence and cannot simultaneously discover equivalence and subsumption mappings. In this paper, we introduce Hybrid Ontology Matching (HOM), a new OM task that unifies equivalence and subsumption discovery, and accordingly propose a Large Language Model (LLM)-based multi-agent OM framework AgentMap that is implemented by a series of interdependent semantic decisions. Given a concept in the source ontology, AgentMap integrates semantic retrieval, hierarchical search, and collaborative multi-agent LLM reasoning to progressively explore the target ontology, identifying either the equivalent concept, if one exists, or the most fine-grained subsumer. We further extend four OM datasets for a HOM benchmark and evaluate AgentMap under hybrid, equivalence-only, and subsumption-only settings. Experimental results show that AgentMap achieves promising performance on the hybrid setting, and at the same time outperforms equivalence matching and subsumption matching baselines on the equivalence-only and subsumption-only settings, respectively.