113 citations · 399 across the 8 of their papers we have counts for
8 papers
AI-assisted pre-review of open-source software submissions: an experience report from BOSC 2026
Tazro Ohta, Nomi L. Harris, Seth Carbon
Most conferences rely on peer-review of submissions, but as generative AI makes it easier than ever to prepare submission materials, some conferences are seeing an overwhelming sur…
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…
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,…
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…
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…
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…