4 papers
mcp-proto-okn: Natural-language access to open scientific knowledge graphs through the Model Context Protocol
Peter W. Rose, Benjamin M. Good, Amanda M. Saravia-Butler +7
MCP Server Proto-OKN (mcp-proto-okn) is a Python-based Model Context Protocol server that enables AI assistants to discover, inspect, query and integrate scientific knowledge graph…
Frontier LLM-based agents can overcome the ontology curation bottleneck for natural phenotypes
James P. Balhoff, Hilmar Lapp
Linking free-text phenotype descriptions to ontology terms, typically referred to as phenotype annotation, is essential for the cross-study integration of comparative morphological…
The Cell Ontology in the age of single-cell omics
Shawn Zheng Kai Tan, Aleix Puig-Barbe, Damien Goutte-Gattat +32
Single-cell omics technologies have transformed our understanding of cellular diversity by enabling high-resolution profiling of individual cells. However, the unprecedented scale…
BioCLIP 2: Emergent Properties from Scaling Hierarchical Contrastive Learning
Jianyang Gu, Samuel Stevens, Elizabeth G Campolongo +13
Foundation models trained at scale exhibit remarkable emergent behaviors, learning new capabilities beyond their initial training objectives. We find such emergent behaviors in bio…