cs.AIApr 2, 2026

The AnIML Ontology: Enabling Semantic Interoperability for Large-Scale Experimental Data in Interconnected Scientific Labs

Authors: Wilf Morlidge, Elliott Watkiss-Leek, George Hannah, Harry Rostron, Andrew Ng, Ewan Johnson, Andrew Mitchell, Terry R. Payne, 

Organizations: School of Computer Science & Informatics, University of Liverpool, UK · Unilever Plc. Materials Innovation Factory, University of Liverpool, UK

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Abstract

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.

Figures & tables

Figure 1: Overview of the AnIML Core module using the Graffoo notation [ 22 ] : yellow boxes denote classes, blue/green arrows are object/datatype properties, purple circles are individuals, green polygons are datatypes. We also denote ODP reuse using grey boxes.
Figure 2: The AnIML technique module.
Figure 3: The AnIML reference pattern.
#Negative RequirementAPMechanism
1No cycles in directlyPrecedes / directlyFollowsAssCycCycle detection
2Nothing may both directly follow and directly precede anything elseAssCycMutual-inverse check
3A reference may not point to a member unless its reference set points to the containing structureRelSpecScope alignment
4A HumanAgent may not have an OS or versionBinOverProperty exclusion
5A HardwareAgent may not have a phone or emailBinOverProperty exclusion
6A HardwareAgent may not be assigned an author role aRelOverRole–type restriction
Table 1: Adversarial competency questions mapped to ontological anti-pattern categories [ 53 ] . AP abbreviations: AssCyc = Association Cycle; BinOver = Binary Relation Between Overlapping Types; RelOver = Relator Mediating Overlapping Types; RelSpec = Relation Specialization; ImpAbs = Imprecise Abstraction; RepRel = Repeatable Relator Instances. All SHACL shapes and test data are in the repository.

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