Ontologies for Behavior. - Peter E. Midford (Bioinform., 2004)

Employing Reasoning within the Phenoscape Knowledgebase. - James P. Balhoff; Wasila M. Dahdul; Hilmar Lapp; Peter E. Midford; Todd J. Vision; Monte Westerfield; Paula M. Mabee (ICBO, 2011)

Integrating Anatomy and Phenotype Ontologies with Taxonomic Hierarchies. - James P. Balhoff; Peter E. Midford; Hilmar Lapp (ICBO, 2011)

Phenoscape: Use Cases and Anatomy Ontology Requirements for Linking Evolutionary and Model Organism Phenotypes. - Wasila M. Dahdul; James P. Balhoff; Hilmar Lapp; Peter E. Midford; Todd J. Vision; Monte Westerfield; Paula M. Mabee (ICBO, 2011)

The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes. - Peter E. Midford; Thomas Dececchi; James P. Balhoff; Wasila M. Dahdul; Nizar Ibrahim; Hilmar Lapp; John G. Lundberg; Paula M. Mabee; Paul C. Sereno; Monte Westerfield; Todd J. Vision; David C. Blackburn (J. Biomed. Semant., 2013)

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. - Arlin Stoltzfus; Hilmar Lapp; Naim Matasci; Helena F. Deus; Brian Sidlauskas; Christian M. Zmasek; Gaurav Vaidya; Enrico Pontelli; Karen Cranston; Rutger A. Vos; Campbell O. Webb; Luke J. Harmon; et al. (BMC Bioinform., 2013)

The MetaCyc database of metabolic pathways and enzymes. - Ron Caspi; Richard Billington; Carol A. Fulcher; Ingrid M. Keseler; Anamika Kothari; Markus Krummenacker; Mario Latendresse; Peter E. Midford; Quang Ong; Wai Kit Ong; Suzanne M. Paley; Pallavi Subhraveti; et al. (Nucleic Acids Res., 2018)

The BioCyc collection of microbial genomes and metabolic pathways. - Peter D. Karp; Richard Billington; Ron Caspi; Carol A. Fulcher; Mario Latendresse; Anamika Kothari; Ingrid M. Keseler; Markus Krummenacker; Peter E. Midford; Quang Ong; Wai Kit Ong; Suzanne M. Paley; et al. (Briefings Bioinform., 2019)

Taxonomic weighting improves the accuracy of a gap-filling algorithm for metabolic models. - Wai Kit Ong; Peter E. Midford; Peter D. Karp (Bioinform., 2020)

The MetaCyc database of metabolic pathways and enzymes - a 2019 update. - Ron Caspi; Richard Billington; Ingrid M. Keseler; Anamika Kothari; Markus Krummenacker; Peter E. Midford; Wai Kit Ong; Suzanne M. Paley; Pallavi Subhraveti; Peter D. Karp (Nucleic Acids Res., 2020)

Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology. - Peter D. Karp; Peter E. Midford; Richard Billington; Anamika Kothari; Markus Krummenacker; Mario Latendresse; Wai Kit Ong; Pallavi Subhraveti; Ron Caspi; Carol A. Fulcher; Ingrid M. Keseler; Suzanne M. Paley (Briefings Bioinform., 2021)