Ontology-aligned structuring and reuse of multimodal materials data and workflows towards automatic reproduction

TL;DR

This paper presents an ontology-driven, LLM-assisted framework for extracting, structuring, and aligning computational workflows from materials science literature to enhance reproducibility and reuse of data.

Contribution

It introduces a novel multi-stage filtering and prompt-engineering approach for automated extraction of workflows, aligned with ontologies to enable knowledge graph construction.

Findings

Successfully extracted workflows from literature using LLMs

Constructed a materials knowledge graph for SFE calculations

Improved transparency and reusability of computational data

Abstract

Reproducibility of computational results remains a challenge in materials science, as simulation workflows and parameters are often reported only in unstructured text and tables. While literature data are valuable for validation and reuse, the lack of machine-readable workflow descriptions prevents large-scale curation and systematic comparison. Existing text-mining approaches are insufficient to extract complete computational workflows with their associated parameters. An ontology-driven, large language model (LLM)-assisted framework is introduced for the automated extraction and structuring of computational workflows from the literature. The approach focuses on density functional theory-based stacking fault energy (SFE) calculations in hexagonal close-packed magnesium and its binary alloys, and uses a multi-stage filtering strategy together with prompt-engineered LLM extraction applied to method sections and tables. Extracted information is unified into a canonical schema and aligned with established materials ontologies (CMSO, ASMO, and PLDO), enabling the construction of a knowledge graph using atomRDF. The resulting knowledge graph enables systematic comparison of reported SFE values and supports the structured reuse of computational protocols. While full computational reproducibility is still constrained by missing or implicit metadata, the framework provides a foundation for organizing and contextualizing published results in a semantically interoperable form, thereby improving transparency and reusability of computational materials data.