Achieving semantic interoperability across heterogeneous experimental data systems remains a major barrier to data-driven scientific discovery. The Analytical Information Markup Language (AnIML), a flexible XML-based standard for analytical chemistry and biology, is increasingly used in industrial R&D labs for managing and exchanging experimental data. However, the expressivity of the XML schema permits divergent interpretations across stakeholders, introducing inconsistencies that undermine the interoperability the AnIML schema was designed to support. In this paper, we present the AnIML Ontology , an OWL 2 ontology that formalises the semantics of AnIML and aligns it with the Allotrope Data Format to support future cross-system and cross-lab interoperability. The ontology was developed using an expert-in-the-loop approach combining LLM-assisted requirement elicitation with collaborative ontology engineering. We validate the ontology through a multi-layered approach: data-driven transformation of real-world AnIML files into knowledge graphs, competency question verification via SPARQL, and a novel validation protocol based on adversarial negative competency questions mapped to established ontological anti-patterns and enforced via SHACL constraints.

Ontology modularization has received growing interest from the research community lately, since it supports tasks such as ontology design/reuse and knowledge selection and integration. Most of the research efforts have concentrated on approaches to extract modules, or generate partitions from an ontology. However these approaches are influenced by different definitions of ontology modularization and thus tend to vary w.r.t. the concepts and properties in the ontology that should define the module, and on the characteristics that modules should exhibit, which often depend on the task for which the modularization process is performed. This diversity of approaches makes the comparative evaluation of the output of different modularization processes hard to perform. In this paper, we propose an entropy inspired measure for modularization, Integrated Ontology Entropy, that approximates the information content of modules, and hence provides a profile for the module generated. This measure is independent of the modularization technique used, and is calculated as a function of the number of edges connecting the named concepts in the ontology, when a graph representation of the ontology is utilized. In the paper we apply this measure to different modularization techniques and we empirically show how the measure captures different characteristics of modules, such as the degree of redundancy and the level of connectedness.

In this paper we therefore propose a reformulation of the entropy metric to evaluate the amount of information carried by both the ontology structure, and also by the language elements (i.e. the semantics associated with the edges in the ontological graph). To evaluate this approach, the reformulated metric is empirically compared to Calemt & Daemi's original entropy metric, for a variety of different sized modules. The results suggest that not only can entropy differentiate between structurally different modules of the same size, but that our improved entropy metric provides a finer grain differentiation than the original entropy metric.

Changes in an ontology may have a disruptive impact on any system using it. This impact may depend on structural changes such as introduction or removal of concept definitions, or it may be related to a change in the expected performance of the reasoning tasks. As the number of systems using ontologies is expected to increase, and given the open nature of the semantic Web, introduction of new ontologies and modifications to existing ones are to be expected. Dynamically handling such changes, without requiring human intervention, becomes crucial. This paper presents a framework that isolates groups of related axioms in an OWL ontology, so that a change in one or more axioms can be automatically localised to a part of the ontology.

To support standardization and tool support of OWL-S, a formal semantics of the language is highly desirable. In this paper, we present a formal Object-Z semantics of OWL-S. This model not only provides a formal unambiguous model which can be used to develop tools and facilitate future development, but as demonstrated in the paper, can be used to identify and eliminate errors in the current documentation.

Interface agents are being developed to assist users with a variety of tasks. To perform effectively, such agents need knowledge of user preferences. An agent architecture has been developed which observes a user performing tasks, and identifies features which can be used as training data by a learning algorithm. Using the learned profile, an agent can give advice to the user on dealing with new situations. The architecture has been applied to two different information filtering domains: classifying incoming mail messages (Magi) and identifying interesting USENet news articles (UNA). This paper describes the architecture and examines the results of experimentation with different learning algorithms and different feature extraction strategies within these domains.