Senior scientific database curator, Artificial Intelligence Center
Ron Caspi, Ph.D., is a biologist working as a database curator in the field of bioinformatics. He has a broad knowledge of biochemistry, metabolism, and molecular biology, which he has been applying since 2004 towards curation of thousands of metabolic pathways, reactions, and enzymes in MetaCyc, the largest and richest metabolic knowledge base available. He has also curated numerous organism-specific Pathway/Genome Databases for important microbes that are part of the BioCyc database collection.
Dr. Caspi is a member of the Enzyme Commission (EC), an international group formed in 1958 to ensure proper naming of enzymes and is the secretary of the IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN).
Dr. Caspi received his B.Sc. cum laude in geology and biology from the Hebrew University in Jerusalem and his PhD in marine microbiology and molecular biology from the Scripps Institution of Oceanography, University of California in San Diego.
Key projects
- The MetaCyc database of metabolic pathways and enzymes
- The BioCyc collection of Pathway/Genome Databases
Recent publications
-
An Evaluation of ChatGPT and Bard (Gemini) in the Context of Biological Knowledge Retrieval
We evaluate the effectiveness of chatbots in retrieving biological knowledge for curation and research purposes.
-
The EcoCyc Database (2023)
The long-term goal of the project is to describe the complete molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to…
-
BioCyc: Metabolic Pathway Databases and Informatics Tools
This article describes a coordinated set of bioinformatics databases and software tools designed to solve multiple problems faced by metabolic engineers and microbiologists related to metabolic pathways.
-
The EcoCyc Database in 2021
This article highlights recent improvements to the curated data in the areas of metabolism, transport, DNA repair, and regulation of gene expression.
-
Pathway Size Matters: The Influence of Pathway Granularity on Over-Representation (Enrichment) Statistics
We show that alternative pathway definitions can alter enrichment p -values by up to nine orders of magnitude, whereas statistical corrections typically alter enrichment p -values by only two orders…
-
Prediction of Selected Biosynthetic Pathways for the Lipopolysaccharide Components in Porphyromonas gingivalis
We use bioinformatics tools to predict biosynthetic pathways for the production of the normal (O-type) lipopolysaccharide in the W50 strain Porphyromonas gingivalis and compare the pathway with other putative pathways…