53 citations · 65 across the 13 of their papers we have counts for
13 papers
Agents for Everyone: A Workshop Framework for Building Agentic AI Capabilities in a Distributed Curation Community
Seth Carbon, Sierra Moxon, Kimberly Van Auken +2
Agentic AI has the potential to accelerate curation of biological databases and knowledge bases. However, uptake has been hindered by a number of challenges and obstacles, includin…
SchemaLink: An Intelligent Web Editor for LinkML Schema Curation
Emanuele Cavalleri, Paolo Perlasca, J. Harry Caufield +3
Motivation: LinkML is a suitable language for the representation of the structural and content constraints of different kinds of biomedical data. Even if it is a quite recent propo…
LinkML: An Open Data Modeling Framework
Sierra A. T. Moxon, Harold Solbrig, Nomi L. Harris +33
Scientific research relies on well-structured, standardized data; however, much of it is stored in formats such as free-text lab notebooks, non-standardized spreadsheets, or data r…
Why we need all the organisms: an exploration of the Monarch knowledge graph to aid mechanism discovery
Katherina Cortes, Daniel Korn, Sarah Gehrke +12
Research done using model organisms has been fundamental to the biological understanding of human genes, diseases and phenotypes. Model organisms provide tractable systems for expe…
Koza and Koza-Hub for born-interoperable knowledge graph generation using KGX
Daniel R Korn, Patrick Golden, Aaron Odell +10
Knowledge graph construction has become an essential domain for the future of biomedical research. But current approaches demand a high amount of redundant labor. These redundancie…
A Dynamic Framework for Semantic Grouping of Common Data Elements (CDE) Using Embeddings and Clustering
Madan Krishnamurthy, Daniel Korn, Melissa A Haendel +2
This research aims to develop a dynamic and scalable framework to facilitate harmonization of Common Data Elements (CDEs) across heterogeneous biomedical datasets by addressing cha…
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…
The Vertebrate Breed Ontology: Towards Effective Breed Data Standardization
Kathleen R. Mullen, Imke Tammen, Nicolas A. Matentzoglu +13
Background: Limited universally-adopted data standards in veterinary medicine hinder data interoperability and therefore integration and comparison; this ultimately impedes the app…
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…
Automated Annotation of Scientific Texts for ML-based Keyphrase Extraction and Validation
Oluwamayowa O. Amusat, Harshad Hegde, Christopher J. Mungall +5
Advanced omics technologies and facilities generate a wealth of valuable data daily; however, the data often lacks the essential metadata required for researchers to find and searc…
An evaluation of GPT models for phenotype concept recognition
Tudor Groza, Harry Caufield, Dylan Gration +5
Objective: Clinical deep phenotyping and phenotype annotation play a critical role in both the diagnosis of patients with rare disorders as well as in building computationally-trac…
GRAPE for Fast and Scalable Graph Processing and random walk-based Embedding
Luca Cappelletti, Tommaso Fontana, Elena Casiraghi +8
Graph Representation Learning (GRL) methods opened new avenues for addressing complex, real-world problems represented by graphs. However, many graphs used in these applications co…