SFE-O: An Ontology for Knowledge-Grounded AI in Supercritical CO$_2$ Biomass Extraction and Fractionation

The Materials Science and Engineering ontology landscape is fragmented along multiple axes simultaneously. Horizontally: a recent survey identified 94 ontologies of which over 40 are structurally incompatible; each new application domain -- ceramics, polymers, batteries, smart materials -- typically restarts ontology design from scratch. Vertically: EU regulation (CSRD, CSDDD, PPWR, CBAM, R2R, AI Act, ESPR) forces material, manufacturing, supply-chain, and lifecycle data into integrated digital product passports, leaving ontologies that only address horizontal fragmentation incomplete for any contemporary consumer. And mechanistically: a vocabulary that records that BNT-BT has $d_{33} \approx 580$ pC/N stores a fact but cannot surface why -- Bi-6s$^2$ lone-pair stereo-activity, anomalous Born effective charges, soft modes, defect chemistry -- without a systematic explanation skeleton. We propose a multi-level modular architecture with two independent classification axes -- level of abstraction (L0 bridges, L1 material-agnostic laboratory-notebook, L2 material-class-specific, L3 categorical reasoning) and consumer audience (material vs. compliance) -- in which the material-specific level is internally organised by a seven-tier mechanistic-explanation skeleton (Symmetry, Energy/DFT, Thermo/CALPHAD, Kinetics, Microstructure, Defect chemistry, Bonding) applicable to any crystalline ionic oxide. The level-and-audience modularity dissolves the horizontal fragmentation, the compliance audience absorbs the vertical regulation pressure, and the seven-tier organisation of Level 2 delivers the mechanistic explanation depth. We instantiate the architecture as the OntoCrafter Ceramics Ontology (OCO v0.94): 5,196 classes across 44 modules; 167,348 OWL axioms (40,454 logical); 1,674 properties; 829 cross-ontology bridge mappings; 1,172 SHACL shapes; 163 published competency questions.

Materials literature contains detailed experimental knowledge, but procedures, chemical entities and measurements remain difficult to aggregate because they are reported in heterogeneous forms and depend on process-specific context. We present SciKGExtract, a schema-guided framework that combines large-language-model extraction with chemical normalization and agent-based evaluation and refinement before knowledge-graph integration. We evaluate the framework on 176 atomic-layer-deposition papers describing zinc oxide (ZnO) and indium--gallium--zinc oxide (IGZO), together with an expert-annotated full-schema subset. PubChem normalization improves exact-match extraction F1 for every tested model. For ZnO, the best F1 increases from 0.591 for direct normalized extraction to 0.805 with agentic refinement, whereas the best IGZO result is 0.344, revealing the greater difficulty of multicomponent supercycle processes. Evaluation against a deeply nested schema containing 65 experimental properties and 155 quantitative measurement nodes further exposes errors in process segmentation and numerical assignment. These results show that chemical canonicalization and targeted agentic verification provide complementary controls for converting complex materials literature into reusable, machine-actionable experimental knowledge.

Scientific literature in materials physics is growing faster than researchers can manually inspect it, yet most retrieval tools rely on keyword matching or generic question answering that ignores domain-specific structure in PDF files. This paper presents an end-to-end pipeline that transforms arXiv superconductivity publications into a searchable corpus with structured metadata and retrieval-augmented question answering. The system combines thematic corpus construction, domain-aware extraction of materials and superconducting transition temperatures, and hybrid retrieval that merges dense chunk embeddings with structured publication fields. We test whether normalized domain attributes improve evidence retrieval and answer groundedness relative to lexical-only and dense text-only methods. Extraction is evaluated on a manually verified gold set of 59 superconducting materials, 46 of which have confirmed experimental critical temperatures. On the 33-material primary positive subset, domain-aware pair accuracy reaches 45.5% versus 9.1% for a regex baseline. Retrieval and generation are compared under a fixed language model (qwen2.5:7b-instruct) on a 100-question benchmark, varying only the retrieval mechanism: BM25, dense, hybrid, and hybrid with domain metadata. BM25 gives the highest source recall (Recall@5 of 47%), and adding extracted metadata to hybrid retrieval does not improve it (39% versus 41%), which we attribute to noise in the extracted fields; the main bottleneck is locating the supporting span inside a correctly retrieved paper. As a materials-informatics application, literature-derived temperatures are matched to an independent theoretical reference set: 200 materials appear in both sources, and 20 have a median experimental critical temperature above the theoretical value.