This page summarizes the many past and present contributors to the EcoCyc project,
and lists the data sources from which EcoCyc integrates data.
Roles: Curation, software development, web site operations
- Peter D. Karp, Bioinformatics Director
- Ingrid Keseler
- Wai Kit Ong
- Suzanne Paley
- Carol Fulcher
- Ron Caspi
- Anamika Kothari
- Markus Krummenacker
- Mario Latendresse
- Pallavi Subhraveti
- Richard Billington
- 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
- Alberto Santos-Zavaleta
- César Bonavides-Martinez
- Luis Muñiz-Rascado
Special reviewers evaluate EcoCyc for accuracy, comprehensiveness, and
clarity in subject areas related to their expertise and recommend
changes in content and presentation.
- William Margolin, University of Texas, Houston: Cell division.
- John Cronan, University of Illinois: Lipid metabolism.
- Jonathan Eisen, TIGR: DNA repair.
- Robert Gunsalus, UCLA: Electron transport.
Past EcoCyc Contributors
Monica Riley |
Milton Saier |
John Ingraham |
Past EcoCyc Developers
- Tomer Altman
- Martha Arnaud
- Joan Chen
- Bruno Contreras-Moreira
- Karen Farquhar
- Mark Hance
- Aaron Johnson
- Aya Kubo
- Irma Martinez Flores
- Laura Nolan
- Alida Pellegrini-Toole
- Monica Ivone Peñaloza-Spinola
- Martin Peralta-Gil
- John Pick
- Qinghu Ren
- Malabika Sarker
- Alexander Shearer
- Can Tran
- Mike Travers
- Dan Weaver
- Deepika Weerasinghe
- Verena Weiss
- Nelson Yang
Other EcoCyc Contributors
- Edward A. Adelberg, Yale University
- Narinder Whitehead, Yale University: Screening and classification of new publications.
EcoCyc Steering Committee
The EcoCyc Steering Committee 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 Steering Committee are listed here.
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
- 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,
- 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.