EcoCyc Credits

This page summarizes the many past and present contributors to the EcoCyc project, lists the data sources from which EcoCyc integrates data, and lists the funding sources for EcoCyc.

EcoCyc Developers

SRI International

Roles: Curation, software development, web site operations.

• Peter D. Karp, Bioinformatics Director
• Suzanne Paley
• Ron Caspi
• Anamika Kothari
• Markus Krummenacker
• Lisa Moore
• Pallavi Subhraveti
• Peter Midford

Macquarie University, Sydney, Australia

Roles: Curation of transport and membrane proteins, lipoproteins, protein secretion, pilus/fimbriae biogenesis, signal transduction systems, DNA repair.

• Ian Paulsen, Subject Editor for Transport
• Liam Elbourne
• Amanda Mackie

Center for Genomic Sciences, Universidad Nacional Autónoma de México (UNAM) -- National Autonomous University of Mexico

Roles: Primary curation of transcriptional regulation of gene expression and operon organization. Contribution to the design of graphical user interfaces displaying this information in EcoCyc and Pathway Tools.

• Julio Collado-Vides, Subject Editor for Transcriptional Regulation
• Socorro Gama-Castro
• César Bonavides-Martinez
• Luis Muñiz-Rascado
• Paloma Lara

The E. coli Whole-Cell Modeling Project at Stanford University: Ecocyc Interface Team

• Markus Covert
• Gwanggyu Sun
• Travis Horst
• Heejo Choi

Special Reviewers

Special reviewers have evaluated EcoCyc for accuracy, comprehensiveness, and clarity in subject areas related to their expertise and recommended changes in content and presentation.

• Robert Gunsalus, UCLA: Electron transport.

• Alan Wolfe, Loyola University Chicago: Acetylation.

Past EcoCyc Contributors

Editors Emeriti

• Monica Riley, Marine Biological Laboratory
• Milton Saier, UC San Diego
• John Ingraham, UC Davis
• Rob Gunsalus, UCLA

Past EcoCyc Developers

• Tomer Altman
• Martha Arnaud
• Richard Billington
• Joan Chen
• Bruno Contreras-Moreira
• Karen Farquhar
• Carol Fulcher
• Mark Hance
• Aaron Johnson
• Ingrid Keseler
• Aya Kubo
• Irma Martinez Flores
• Laura Nolan
• Wai Kit Ong
• Alida Pellegrini-Toole
• Monica Ivone Peñaloza-Spinola
• Martin Peralta-Gil
• John Pick
• Qinghu Ren
• Alberto Santos-Zavaleta
• Malabika Sarker
• Alexander Shearer
• Can Tran
• Mike Travers
• Dan Weaver
• Deepika Weerasinghe
• Verena Weiss
• Nelson Yang

EcoCyc Advisory Board

The EcoCyc Advisory Board advises the project on a variety of matters including task prioritization, database content, user interface issues, and community outreach. The committee meets once per year.

Current and former members of the advisory board are listed here.

Sources of Data Integrated into EcoCyc

EcoCyc incorporates information that was obtained from several sources. EcoCyc publications describe the integration of data from these sources in more detail. Those sources are as follows.

• Genbank record U00096 produced by the Blattner laboratory, October, 1997. This Genbank record was the source of the original E. coli MG1655 genome sequence and annotation incorporated by EcoCyc. A corrected nucleotide sequence was deposited in GenBank as U00096.2 in 2004, and the revised sequence was incorporated into EcoCyc as of version 8.6 (Nov. 2004). The revised genome annotation published in Riley et al. was incorporated into EcoCyc in version 10.0 (March 2006).
  
  EcoCyc is involved in a collaboration to update the genome annotation of the U00096.2 and RefSeq (NC_000913.2) entries for E. coli MG1655 on an ongoing basis. The collaborators include EcoCyc, EcoGene, EcoliHub, the Coli Genetic Stock Center, ASAP/ERIC, RegulonDB, and UniProtKB/Swiss-Prot. The collaborators routinely share their data and resolve conflicts among the data. Those updates are shared among all partners.
  
  However, minor annotation discrepancies may still exist between EcoCyc and these Genbank entries.

• The ENZYME database, developed by A. Bairoch at the Swiss Institute of Bioinformatics. This database is based on reactions that were originally defined by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB). Downloaded data includes the Enzyme Nomenclature system that classifies enzymatically catalyzed reactions.

• PubMed -- Many literature citations within EcoCyc are obtained from PubMed.

• UniProt Gene Ontology data -- We regularly integrate Gene Ontology annotations from UniProt into EcoCyc. These data are combined with internal Gene Ontology terms curated by EcoCyc, as follows:
  • If EcoCyc gene G already has GO term T, we do not add to G the annotations from UniProt to the same term (unless they differ in Evidence Code, Db-Reference, or With field)
  • If UniProt contains term T1 for gene G, and EcoCyc already contains term T2 for G, and T1 is an Is-A parent of T2 in the GO hierarchy, and the only annotations for T1 have evidence code IEA, and for all of these T1 annotations, there are also annotations on T2 with evidence code IEA and the same Db-Reference and With fields, then we do not add term T1 to EcoCyc for G. In other words, if a less specific term T1 only has computational evidence that is duplicated by annotations to a more specific term T2, we leave away T1.

• UniProt protein feature data -- Starting with EcoCyc version 13.0 (2009), protein feature information from UniProt will be periodically loaded into EcoCyc. UniProt protein feature data are imported into EcoCyc using the following criteria:
  • If the sequence data for the UniProt protein and the EcoCyc protein do not match for the region or residues of a protein feature, then the feature is not loaded.
  • If a protein feature of the same type and location already exists for a EcoCyc protein, then the UniProt protein feature is not imported.
  • UniProt protein features related to topological domains, non-terminal residues, non-consecutive residues, and secondary structure are excluded.
  • UniProt protein features of type 'Chain' which span the entire length of the protein are excluded.

Data extracted from UniProt is copyright of the UniProt Consortium and subject to the Creative Commons Attribution (CC BY 4.0) License and the disclaimers at uniprot.org/help/license. The original data is available from uniprot.org.

EcoCyc Funding Sources

EcoCyc is supported by the NIH National Institute of General Medical Sciences under grant GM077678.

The Pathway Tools software behind EcoCyc is supported by the NIH National Institute of Allergy and Infectious Diseases under grant AI160719.