113 citations · 213 across the 7 of their papers we have counts for
7 papers
The Artificial Intelligence Ontology: LLM-assisted construction of AI concept hierarchies
Marcin P. Joachimiak, Mark A. Miller, J. Harry Caufield +5
The Artificial Intelligence Ontology (AIO) is a systematization of artificial intelligence (AI) concepts, methodologies, and their interrelations. Developed via manual curation, wi…
Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI)
Sabrina Toro, Anna V Anagnostopoulos, Sue Bello +27
Background: Ontologies are fundamental components of informatics infrastructure in domains such as biomedical, environmental, and food sciences, representing consensus knowledge in…
An Open-Source Knowledge Graph Ecosystem for the Life Sciences
Tiffany J. Callahan, Ignacio J. Tripodi, Adrianne L. Stefanski +29
Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these…
Gene Set Summarization using Large Language Models
Marcin P. Joachimiak, J. Harry Caufield, Nomi L. Harris +2
Molecular biologists frequently interpret gene lists derived from high-throughput experiments and computational analysis. This is typically done as a statistical enrichment analysi…
Structured prompt interrogation and recursive extraction of semantics (SPIRES): A method for populating knowledge bases using zero-shot learning
J. Harry Caufield, Harshad Hegde, Vincent Emonet +9
Creating knowledge bases and ontologies is a time consuming task that relies on a manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases,…
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,…
Developing a Knowledge Graph Framework for Pharmacokinetic Natural Product-Drug Interactions
Sanya B. Taneja, Tiffany J. Callahan, Mary F. Paine +4
Pharmacokinetic natural product-drug interactions (NPDIs) occur when botanical natural products are co-consumed with pharmaceutical drugs. Understanding mechanisms of NPDIs is key…