FlyAOC: Evaluating Agentic Ontology Curation of Drosophila Scientific Knowledge Bases

arXiv:2602.09163 · cs.AI, cs.CL, cs.IR · Submitted 2026-02-09 · Read on arXiv

cs.AI, cs.CL, cs.IR

Submitted: 2026-02-09

Updated: 2026-09-25

Code: https://github.com/xingjian-zhang/flyaoc

Terminology

• Ontology — 89× in this paper · explained in 2 episodes
• Benchmark — 36× in this paper · explained in 2 episodes
• Gene Ontology — 35× in this paper
• Agent Architectures — 12× in this paper · explained in 1 episode
• Semantic Similarity — 6× in this paper · explained in 2 episodes
• Perplexity — 5× in this paper · explained in 3 episodes
• Accuracy — 4× in this paper · explained in 1 episode
• AI Agents — 3× in this paper · explained in 2 episodes
• Grounding — 3× in this paper · explained in 3 episodes
• Agentic Framework — 2× in this paper · explained in 6 episodes
• Aggregation — 2× in this paper · explained in 1 episode
• Multi-Agent System — 2× in this paper · explained in 6 episodes
• Trace — 2× in this paper · explained in 2 episodes
• Adaptation — 1× in this paper · explained in 1 episode
• Agentic Architecture — 1× in this paper · explained in 1 episode
• Agentic Reasoning — 1× in this paper · explained in 1 episode
• Agentic Workflows — 1× in this paper · explained in 1 episode
• Arabidopsis Information Resource — 1× in this paper
• Benchmarking — 1× in this paper · explained in 3 episodes
• Commentary — 1× in this paper · explained in 2 episodes
• Computational Biology — 1× in this paper · explained in 2 episodes
• Dynamic Adaptation — 1× in this paper · explained in 2 episodes
• Failure Modes — 1× in this paper · explained in 3 episodes
• Fidelity — 1× in this paper · explained in 2 episodes
• Hallucination — 1× in this paper · explained in 3 episodes
• Hybrid Architectures — 1× in this paper · explained in 3 episodes
• Large Language Models (LLMs) — 1× in this paper · explained in 6 episodes
• Provenance — 1× in this paper · explained in 4 episodes
• Verification — 1× in this paper · explained in 2 episodes

Sources

• CurateGPT: A flexible language-model assisted biocuration tool
• Structured prompt interrogation and recursive extraction of semantics (SPIRES): A method for populating knowledge bases using zero-shot learning
• STRUCTSENSE: A Task-Agnostic Agentic Framework for Structured Information Extraction with Human-In-The-Loop Evaluation and Benchmarking
• DeepResearch Bench: A Comprehensive Benchmark for Deep Research Agents
• Simple Is Effective: The Roles of Graphs and Large Language Models in Knowledge-Graph-Based Retrieval-Augmented Generation
• ReportBench: Evaluating Deep Research Agents via Academic Survey Tasks
• Humanity's Last Exam

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