A Storage System for Scalable Knowledge Representation (2007)
Karp, Peter D., Paley, Suzanne M., Greenberg, Ira
Twenty years of AI research in knowledge representation has produced frame knowledge representation systems (FRSs) that incorporate a number of important advances. However, FRSs lack two important...
Representations of Metabolic Knowledge: Pathways (2001)
Peter D. Karp, Suzanne M. Paley
The automatic generation of drawings of metabolic pathways is a challenging problem that depends intimately on exactly what information has been recorded for each pathway, and on how that information...
The EcoCyc and MetaCyc Databases (2000)
Peter D. Karp, Monica Riley, Milton Saier, Ian T. Paulsen, Suzanne M. Paley
EcoCyc is an organism-specific Pathway/Genome Database that describes the metabolic and signal-transduction pathways of E. coli, its enzymes, and --- a new addition --- its transport proteins....
A Collaborative Environment for Authoring Large Knowledge Bases (2000)
Peter D. Karp, Vinay K. Chaudhri, Suzanne M. Paley
Collaborative knowledge base (KB) authoring environments are critical for the construction of high-performance KBs. Such environments must support rapid construction of KBs by a collaborative effort...
A Generic Knowledge-Base Browser and Editor (2000)
Suzanne M. Paley, John D. Lowrance, Peter D. Karp
1 The GKB Editor is a generic editor and browser of knowledge bases (KBs) and ontologies --- generic in the sense that it is portable across several frame knowledge representation systems (FRSs)....
EcoCyc: Encyclopedia of E. coli Genes and Metabolism (1999)
Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-toole, Markus Krummenacker
1 The EcoCyc database describes the genome and gene products of E. coli, its metabolic and signal-transduction pathways, and its tRNAs. The database describes 4391 genes of E. coli, 695 enzymes...
A Generic Knowledge-Base Browser and Editor. (1998)
Lowrance, John D., Paley, Suzanne M., Karp, Peter D., Olowe, Ife
The Generic KnowledgeBase Editor (EKG-Editor) is a generic editor and browser of KBs and ontologies - generic in the sense that it is portable across several FRSs. This generally is possible because...
EcoCyc User's Guide Version 4.5 (1998)
Ecocyc User's Guide, Peter D. Karp, Suzanne M. Paley, Markus Krummenacker
this document do not apply to the EcoCyc WWW server. Users of that server should read this guide more for general background information about the meaning of the information that is presented, than...
EcoCyc User's Guide Version 4.5 (1998)
Ecocyc User's Guide, Peter D. Karp, Suzanne M. Paley, Markus Krummenacker
this document do not apply to the EcoCyc WWW server. Users of that server should read this guide more for general background information about the meaning of the information that is presented, than...
EcoCyc: Encyclopedia of Escherichia coli genes and metabolism (1997)
Peter D. Karp, Monica Riley, Suzanne M. Paley, Alida Pellegrini-toole, Markus Krummenacker
The encyclopedia of Escherichia coli genes and metabolism (EcoCyc) is a database that combines information about the genome and the intermediary metabolism of E.coli. The database describes 3030...
Representations of Metabolic Knowledge: Pathways (1996)
Peter D. Karp, Suzanne M. Paley
The automatic generation of drawings of metabolic pathways is a challenging problem that depends intimately on exactly what information has been recorded for each pathway, and on how that information...
Retrofitting Existing Applications and Authoring New Applications for the World Wide Web (1995)
Peter D. Karp, Suzanne M. Paley
Introduction The advent of the WWW presents both opportunities and challenges. Information providers now have the means of making their information available to a far larger audience than they had...
Retrofitting Existing Applications and Authoring New Applications for the World Wide Web (1995)
Peter D. Karp, Suzanne M. Paley
Introduction The advent of the WWW presents both opportunities and challenges. Information providers now have the means of making their information available to a far larger audience than they had...
Karp, Peter D., Riley, Monica, Saier, Milton, Paulsen, Ian T., Collado-Vides, Julio, Paley, Suzanne M., ...
EcoCyc is an organism-specific pathway/genome database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, its transport proteins and its mechanisms of...
Karp, Peter D., Riley, Monica, Paley, Suzanne M., Pellegrini-Toole, Alida
MetaCyc is a metabolic-pathway database that describes 445 pathways and 1115 enzymes occurring in 158 organisms. MetaCyc is a review-level database in that a given entry in MetaCyc often integrates...
The EcoCyc and MetaCyc databases
Karp, Peter D., Riley, Monica, Saier, Milton, Paulsen, Ian T., Paley, Suzanne M., Pellegrini-Toole, Alida
EcoCyc is an organism-specific Pathway/Genome Database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, and—a new addition—its transport proteins....
The Pathway Tools cellular overview diagram and Omics Viewer
Paley, Suzanne M., Karp, Peter D.
The Pathway Tools cellular overview diagram is a visual representation of the biochemical network of an organism. The overview is automatically created from a Pathway/Genome Database describing that...
Karp, Peter D., Riley, Monica, Saier, Milton, Paulsen, Ian T., Collado-Vides, Julio, Paley, Suzanne M., ...
EcoCyc is an organism-specific pathway/genome database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, its transport proteins and its mechanisms of...
Karp, Peter D., Riley, Monica, Paley, Suzanne M., Pellegrini-Toole, Alida
MetaCyc is a metabolic-pathway database that describes 445 pathways and 1115 enzymes occurring in 158 organisms. MetaCyc is a review-level database in that a given entry in MetaCyc often integrates...
The EcoCyc and MetaCyc databases
Karp, Peter D., Riley, Monica, Saier, Milton, Paulsen, Ian T., Paley, Suzanne M., Pellegrini-Toole, Alida
EcoCyc is an organism-specific Pathway/Genome Database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, and—a new addition—its transport proteins....
The Pathway Tools cellular overview diagram and Omics Viewer
Paley, Suzanne M., Karp, Peter D.
The Pathway Tools cellular overview diagram is a visual representation of the biochemical network of an organism. The overview is automatically created from a Pathway/Genome Database describing that...
Multidimensional annotation of the Escherichia coli K-12 genome
Karp, Peter D., Keseler, Ingrid M., Shearer, Alexander, Latendresse, Mario, Krummenacker, Markus, Paley, Suzanne M., ...
The annotation of the Escherichia coli K-12 genome in the EcoCyc database is one of the most accurate, complete and multidimensional genome annotations. Of the 4460 E. coli genes, EcoCyc assigns...