Generating Reliable Adverse event Profiles for Health through Automated Integrated Data (GRAPH-AID): A Semi-Automated Ontology Building Approach

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.

VEL: A Formally Verified Reasoner for OWL2 EL Profile

Over the past two decades, the Web Ontology Language (OWL) has been instrumental in advancing the development of ontologies and knowledge graphs, providing a structured framework that enhances the semantic integration of data. However, the reliability of deductive reasoning within these systems remains challenging, as evidenced by inconsistencies among popular reasoners in recent competitions. This evidence underscores the limitations of current testing-based methodologies, particularly in high-stakes domains such as healthcare. To mitigate these issues, in this paper, we have developed VEL, a formally verified EL++ reasoner equipped with machine-checkable correctness proofs that ensure the validity of outputs across all possible inputs. This formalization, based on the algorithm of Baader et al., has been transformed into executable OCaml code using the Coq proof assistant's extraction capabilities. Our formalization revealed several errors in the original completeness proofs, which led to changes to the algorithm to ensure its completeness. Our work demonstrates the necessity of mechanization of reasoning algorithms to ensure their correctness at theoretical and implementation levels.