113 citations · 484 across the 22 of their papers we have counts for
22 papers
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…
Enabling Down Syndrome Research through a Knowledge Graph-Driven Analytical Framework
Madan Krishnamurthy, Surya Saha, Pierrette Lo +5
Trisomy 21 results in Down syndrome, a multifaceted genetic disorder with diverse clinical phenotypes, including heart defects, immune dysfunction, neurodevelopmental differences,…
Improving Biomedical Knowledge Graph Quality: A Community Approach
Katherina G Cortes, Shilpa Sundar, Sarah Gehrke +13
Biomedical knowledge graphs (KGs) are widely used across research and translational settings, yet their design decisions and implementation are often opaque. Unlike ontologies that…
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…
CurateGPT: A flexible language-model assisted biocuration tool
Harry Caufield, Carlo Kroll, Shawn T O'Neil +10
Effective data-driven biomedical discovery requires data curation: a time-consuming process of finding, organizing, distilling, integrating, interpreting, annotating, and validatin…
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…
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…
MapperGPT: Large Language Models for Linking and Mapping Entities
Nicolas Matentzoglu, J. Harry Caufield, Harshad B. Hegde +6
Aligning terminological resources, including ontologies, controlled vocabularies, taxonomies, and value sets is a critical part of data integration in many domains such as healthca…
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…
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,…
Analyzing historical diagnosis code data from NIH N3C and RECOVER Programs using deep learning to determine risk factors for Long Covid
Saurav Sengupta, Johanna Loomba, Suchetha Sharma +5
Post-acute sequelae of SARS-CoV-2 infection (PASC) or Long COVID is an emerging medical condition that has been observed in several patients with a positive diagnosis for COVID-19.…
Ontologizing Health Systems Data at Scale: Making Translational Discovery a Reality
Tiffany J. Callahan, Adrianne L. Stefanski, Jordan M. Wyrwa +29
Background: Common data models solve many challenges of standardizing electronic health record (EHR) data, but are unable to semantically integrate all the resources needed for dee…
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 method for comparing multiple imputation techniques: a case study on the U.S. National COVID Cohort Collaborative
Elena Casiraghi, Rachel Wong, Margaret Hall +34
Healthcare datasets obtained from Electronic Health Records have proven to be extremely useful to assess associations between patients' predictors and outcomes of interest. However…
Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science
Deepak R. Unni, Sierra A. T. Moxon, Michael Bada +21
Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph-based data models elucidate the int…
Beyond Low Earth Orbit: Biomonitoring, Artificial Intelligence, and Precision Space Health
Ryan T. Scott, Erik L. Antonsen, Lauren M. Sanders +53
Human space exploration beyond low Earth orbit will involve missions of significant distance and duration. To effectively mitigate myriad space health hazards, paradigm shifts in d…
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…
An Open Natural Language Processing Development Framework for EHR-based Clinical Research: A case demonstration using the National COVID Cohort Collaborative (N3C)
Sijia Liu, Andrew Wen, Liwei Wang +28
While we pay attention to the latest advances in clinical natural language processing (NLP), we can notice some resistance in the clinical and translational research community to a…