Comprehensive pathway datasets are essential resources for advancing biological research, yet constructing these datasets is labor intensive. Recognizing the labor-intensive nature of constructing these critical resources, we present BioGraphia, a web-based annotation platform designed to facilitate collaborative pathway graph annotation. BioGraphia supports multi-user collaboration with real-time monitoring, curation, and interactive pathway graph visualization. It enables users to directly annotate the nodes and relations on the candidate graph, guided by detailed instructions. The platform is further enhanced with a large language model that automatically generates explainable and span-aligned pre-annotation to accelerate the annotation process. Its modular design allows flexible integration of external knowledge bases, and customization of the definition of annotation schema and, to support adaptation to other graph-based annotation tasks. Code is available at https://github.com/LeiLiLab/BioGraphia

Recent studies have combined Large Language Models (LLMs) with Knowledge Graphs (KGs) to enhance reasoning, improving inference accuracy without additional training while mitigating hallucination. However, existing frameworks still suffer two practical drawbacks: they must be re-tuned whenever the KG or reasoning task changes, and they depend on a single, high-capacity LLM for reliable (i.e., trustworthy) reasoning. To address this, we introduce R2-KG, a plug-and-play, dual-agent framework that separates reasoning into two roles: an Operator (a low-capacity LLM) that gathers evidence and a Supervisor (a high-capacity LLM) that makes final judgments. This design is cost-efficient for LLM inference while still maintaining strong reasoning accuracy. Additionally, R2-KG employs an Abstention mechanism, generating answers only when sufficient evidence is collected from KG, which significantly enhances reliability. Experiments across five diverse benchmarks show that R2-KG consistently outperforms baselines in both accuracy and reliability, regardless of the inherent capability of LLMs used as the operator. Further experiments reveal that the single-agent version of R2-KG, equipped with a strict self-consistency strategy, achieves significantly higher-than-baseline reliability with reduced inference cost but increased abstention rate in complex KGs. Our findings establish R2-KG as a flexible and cost-effective solution for KG-based reasoning, reducing reliance on high-capacity LLMs while ensuring trustworthy inference.