An Ontology-Guided, Deduplication-Aware Extraction Layer for Knowledge Graph Construction from Heterogeneous Documents

Extraction produces candidate entities and relationships; writing them into a graph is where identity is decided, and identity decisions are destructive in a way extraction errors are not. A wrong type can be corrected later, but two records merged under one identity cannot be separated once their properties have been combined, and the merge leaves no error behind. This paper describes the ingestion and ontology-tagging layer that turns a validated extraction stream into a knowledge graph of 537,157 entities and 2,198,567 relationships drawn from 98,795 government documents. We describe a record-identity ladder that decides sameness from identifier columns, name columns, display names and type-scoped position rather than from name similarity. The ladder governs de-duplication within parsed tables, while the graph write applies a coarser canonical-name key, so records sharing a canonical name merge automatically on exact equality. We argue rather than demonstrate that this is where the automation line belongs: no identity benchmark is reported, and the over-merges the key permits are undetectable by construction. That policy, under which entity resolution only ever flags candidates, followed an incident in which two surface forms of one name were merged, corrupting a correct record and deleting eight entities from an unrelated document. We then describe multi-class ontology tagging and an evidence asymmetry we did not anticipate: an entity name is an instance label rather than a type assertion, so matching name fragments against a class index invents classifications. Requiring anchored evidence cut role assignments on an enriched sample from 36 to 4, all confirmed correct. We quantify the graph's conformance debt, show secondary classifications compensating for a mis-parented primary class, and describe a curation queue grown to 48,403 pending proposals against 775 human decisions.

Large language models extracting knowledge graphs from text capture only explicitly stated facts, often leaving semantically related entities disconnected across documents. We present an additive, engine-neutral second pass that discovers these latent ties without altering extracted facts. Each document is chunked and embedded once; top-k nearest- neighbor queries across existing chunks yield candidate node pairs via entity membership maps. Candidate pairs are scored using Shepard inverse-distance weighting with a rescaled chord distance metric, avoiding the threshold-collapsing flaw of affine cosine scoring behind a k-NN gate. Un-gated per-pair accumulators form a commutative monoid, ensuring the pipeline is strictly order-independent and scales incrementally without recomputing prior documents. Implemented across FalkorDB, Kinetica, ArangoDB, and Neo4j, our method shows that 768- and 240-dimensional embeddings retain 92% and 72% edge fidelity against a 3072-D baseline while achieving a 25x faster top-k formulation.

We present a web demo for exploring a large-scale disambiguated knowledge base (KB) materialized from a large language model (LLM). GPTKB 2.0 contains 38.4M triples over 1.6M canonical entities, together with 207.6K consolidated relations and 66K consolidated classes. Unlike prior LLM-derived knowledge bases that largely identify entities by surface strings, GPTKB 2.0 performs context-guided disambiguation during recursive KB construction, separating homonyms and merging synonymous mentions as facts are elicited. The demo makes this process inspectable: users can browse entities, follow links across the KB, and audit the provenance of individual facts, including surface forms, candidate matches, source triples, and disambiguation decisions. The interface further supports structured SPARQL queries, natural-language questions translated to SPARQL, and entity linking from user-provided text to canonical GPTKB 2.0 entries. GPTKB 2.0 is available at https://gptkb.org/, with the full KB downloadable for offline use.