cs.DBFeb 27, 2026

A Pythonic Functional Approach for Semantic Data Harmonisation in the ILIAD Project

Authors: Erik Johan Nystad, Francisco Martín-Recuerda

Organizations: SINTEF Digital, Oslo, Norway

Abstract

Semantic data harmonisation is a central requirement in the ILIAD project, where heterogeneous environmental data must be harmonised according to the Ocean Information Model (OIM), a modular family of ontologies for enabling the implementation of interoperable Digital Twins of the Ocean. Existing approaches to Semantic Data Harmonisation, such as RML and OTTR, offer valuable abstractions but require extensive knowledge of the technical intricacies of the OIM and the Semantic Web standards, including namespaces, IRIs, OWL constructors, and ontology design patterns. Furthermore, RML and OTTR oblige practitioners to learn specialised syntaxes and dedicated tooling. Data scientists in ILIAD have found these approaches overly cumbersome and have therefore expressed the need for a solution that abstracts away these technical details while remaining seamlessly integrated into their Python-based environments. To address these requirements, we have developed a Pythonic functional approach to semantic data harmonisation that enables users to produce correct RDF through simple function calls. The functions, structured as Python libraries, encode the design patterns of the OIM and are organised across multiple levels of abstraction. Low-level functions directly expose OWL and RDF syntax, mid-level functions encapsulate ontology design patterns, and high-level domain-specific functions orchestrate data harmonisation tasks by invoking mid-level functions. According to feedback from ILIAD data scientists, this approach satisfies their requirements and substantially enhances their ability to participate in harmonisation activities. In this paper, we present the details of our Pythonic functional approach to semantic data harmonisation and demonstrate its applicability within the ILIAD Aquaculture pilot.

Figures & tables

Explore similar work

Apr 2, 2026

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

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.
Apr 7, 2026

BDI-Kit Demo: A Toolkit for Programmable and Conversational Data Harmonization

Data harmonization remains a major bottleneck for integrative analysis due to heterogeneity in schemas, value representations, and domain-specific conventions. BDI-Kit provides an extensible toolkit for schema and value matching. It exposes two complementary interfaces tailored to different user needs: a Python API enabling developers to construct harmonization pipelines programmatically, and an AI-assisted chat interface allowing domain experts to harmonize data through natural language dialogue. This demonstration showcases how users interact with BDI-Kit to iteratively explore, validate, and refine schema and value matches through a combination of automated matching, AI-assisted reasoning, and user-driven refinement. We present two scenarios: (i) using the Python API to programmatically compose primitives, examine intermediate outputs, and reuse transformations; and (ii) conversing with the AI assistant in natural language to access BDI-Kit's capabilities and iteratively refine outputs based on the assistant's suggestions.
Aug 8, 2026

H2: A Dual Hybrid Semantic Data Lake Architecture for Medical Data Harmonization with Human-In-the-Loop verified, LLM Driven Metadata Annotation System

Medical data, by its nature, exhibit a high degree of heterogeneity on multiple levels ranging from (a) different modalities like images, text and time series, (b) diverse tabular schemata introduced by institutions and (c) completely unstructured textual information data provided by healthcare professionals. Data lakes are often used in medical data storage to consolidate all heterogeneous diverse data in a single, central location, where it can be saved "as is", without the need to impose a schema like a data warehouse does. Despite their flexibility, though, data lakes are notorious for the "data swamp" failure. Thus, providing a reliable data harmonization mechanism through metadata, without compromising integrity or flexibility, is a real challenge. To this end, knowledge graphs have attracted attention since they provide a dynamic way to depict relationships without a rigid schema-on-write approach. Additionally, another rigorous task relies on the interoperability of data: application of appropriate ML techniques on such a diverse nature of data is not an easy task, as a domain expert must decide the efficacy of a method to a specific data type or dataset. Metadata annotation can aid by tagging applicable operations, however this requires manual intervention, not to mention the plethora of existing datasets which lack such information. To tackle both challenges, in this paper, we propose a semantic data lake architecture that promotes data harmonization and incorporates a generative annotation process (i.e. LLMs) of non-labeled metadata collections to support the application of meaningful ML techniques. Building on top of this approach, we create a higher level of knowledge, identifying suitability of data with respect to applicable ML operations based on their data nature...