113 citations · 405 across the 12 of their papers we have counts for
12 papers
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,…
Perspectives for self-driving labs in synthetic biology
Hector Garcia Martin, Tijana Radivojevic, Jeremy Zucker +19
Self-driving labs (SDLs) combine fully automated experiments with artificial intelligence (AI) that decides the next set of experiments. Taken to their ultimate expression, SDLs co…
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…
Creation and unification of development and life stage ontologies for animals
Anne Niknejad, Christopher J. Mungall, David Osumi-Sutherland +2
With the new era of genomics, an increasing number of animal species are amenable to large-scale data generation. This had led to the emergence of new multi-species ontologies to a…
Guidelines for reporting cell types: the MIRACL standard
Tiago Lubiana, Paola Roncaglia, Christopher J. Mungall +4
Cell types are at the root of modern biology, and describing them is a core task of the Human Cell Atlas project. Surprisingly, there are no standards for reporting new cell types,…
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…
Recommendations for extending the GFF3 specification for improved interoperability of genomic data
Surya Saha, Scott Cain, Ethalinda K. S. Cannon +8
The GFF3 format is a common, flexible tab-delimited format representing the structure and function of genes or other mapped features (https://github.com/The-Sequence-Ontology/Speci…
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…
GOTaxon: Representing the evolution of biological functions in the Gene Ontology
Haiming Tang, Christopher J Mungall, Huaiyu Mi +1
The Gene Ontology aims to define the universe of functions known for gene products, at the molecular, cellular and organism levels. While the ontology is designed to cover all aspe…