The rapid growth of climate science literature necessitates advanced information extraction (IE) systems to structure knowledge for researchers and policymakers. We introduce ClimateIE, a novel framework combining taxonomy-guided large language model (LLM) annotation with expert validation to address three core tasks: climate-specific named entity recognition, relationship extraction, and entity linking. Our contributions include: (1) the ClimateIE-Corpus—500 climate publications annotated via a hybrid human-AI pipeline with mappings to the extended GCMD+ taxonomy; (2) systematic evaluation showing Llama-3.3-70B achieves state-of-the-art performance (strict F1: 0.378 NER, 0.367 EL), outperforming larger commercial models (GPT-4o) and domain-adapted baselines (ClimateGPT) by 11-58%; and (3) analysis revealing critical challenges in technical relationship extraction (MountedOn: 0.000 F1) and emerging concept linking (26.4% unlinkable entities). Upon acceptance, we will release the corpus, toolkit, and guidelines to advance climate informatics, establishing benchmarks for NLP in Earth system science and underscoring the need for dynamic taxonomy governance and implicit relationship modeling.

We present a taxonomy-driven framework for constructing domain-specific knowledge graphs (KGs) that integrates structured taxonomies, Large Language Models (LLMs) and Retrieval-Augmented Generation (RAG). Although we focus on climate science to illustrate its effectiveness, our approach can potentially be adapted for other specialized domains. Existing methods often neglect curated taxonomies—hierarchies of verified entities and relationships—and LLMs frequently struggle to extract KGs in specialized domains. Our approach addresses these gaps by anchoring extraction to expert-curated taxonomies, aligning entities and relations with domain semantics, and validating LLM outputs using RAG against the domain taxonomy. Through a climate science case study using our annotated dataset of 25 publications (1,705 entity-publication links, 3,618 expert-validated relationships), we demonstrate that taxonomy-guided LLM prompting combined with RAG-based validation reduces hallucinations by 23.3% while improving F1 scores by 13.9% compared to baselines without the proposed techniques. Our contributions include: 1) a generalizable methodology for taxonomy-aligned KG construction; 2) a reproducible annotation pipeline, 3) the first benchmark dataset for climate science information retrieval; and 4) empirical insights into combining structured taxonomies with LLMs for specialized domains. The dataset, including expert annotations and taxonomy-aligned outputs, is publicly available at https://github.com/Jo-Pan/ClimateIE, and the accompanying framework can be accessed at https://github.com/Jo-Pan/TaxoDrivenKG.