94 citations · 177 across the 10 of their papers we have counts for
11 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…
VLM4Bio: A Benchmark Dataset to Evaluate Pretrained Vision-Language Models for Trait Discovery from Biological Images
M. Maruf, Arka Daw, Kazi Sajeed Mehrab +19
Images are increasingly becoming the currency for documenting biodiversity on the planet, providing novel opportunities for accelerating scientific discoveries in the field of orga…
Hierarchical Conditioning of Diffusion Models Using Tree-of-Life for Studying Species Evolution
Mridul Khurana, Arka Daw, M. Maruf +12
A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species acr…
Discovering Novel Biological Traits From Images Using Phylogeny-Guided Neural Networks
Mohannad Elhamod, Mridul Khurana, Harish Babu Manogaran +15
Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how…
KG-Hub -- Building and Exchanging Biological Knowledge Graphs
J Harry Caufield, Tim Putman, Kevin Schaper +23
Knowledge graphs (KGs) are a powerful approach for integrating heterogeneous data and making inferences in biology and many other domains, but a coherent solution for constructing,…
Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies
Nicolas Matentzoglu, Damien Goutte-Gattat, Shawn Zheng Kai Tan +24
Similar to managing software packages, managing the ontology life cycle involves multiple complex workflows such as preparing releases, continuous quality control checking, and dep…
A Simple Standard for Sharing Ontological Mappings (SSSOM)
Nicolas Matentzoglu, James P. Balhoff, Susan M. Bello +41
Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representatio…
Presence-absence reasoning for evolutionary phenotypes
James P. Balhoff, T. Alexander Dececchi, Paula M. Mabee +1
Nearly invariably, phenotypes are reported in the scientific literature in meticulous detail, utilizing the full expressivity of natural language. Often it is particularly these de…