BioCyc Credits

This page summarizes the contributors to the BioCyc databases and website, lists data sources from which BioCyc integrates data, and lists third-party computational tools integrated within the BioCyc webiste. These credits do not cover the EcoCyc project, whose credits are listed here.

BioCyc Developers

SRI International

Roles: Curation, software development, web site operations

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

Macquarie University, Sydney, Australia

Roles: Curation

• Ian Paulsen
• Amanda Mackie
• Brendan Wilson-Mortier

Special Reviewers

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

• David S. Weiss (University of Iowa): peptidoglycan synthesis in Clostridioides difficile

Past BioCyc Developers

• Tomer Altman
• Richard Billington
• Joseph M. Dale
• Liam Elbourne
• Fred Gilham
• Michelle Green
• Tim Holland
• Tom Lee
• Mario Latendresse
• John Pick
• Liviu Popescu
• Mike Travers
• Martha Arnaud
• Kate Dreher
• Hartmut Foerster
• Carol A. Fulcher
• John Ingraham
• Irinia Iourovitski
• Ingrid Keseler
• Cynthia J. Krieger
• Varsha Naidu
• Wai Kit Ong
• Anurada Pujar
• Malabika Sarker
• Christopher Tissier
• Miles Trupp
• Deepika Weerasinghe
• Huacheng C. Ying
• Peifen Zhang

BioCyc Advisory Board

The BioCyc 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 BioCyc

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

• Most BioCyc genomes are obtained from the NCBI RefSeq database.

• BioCyc taxonomy information is obtained from the NCBI Taxonomy Database.

• The ExplorEnz database --- downloaded data includes the Enzyme Nomenclature system that classifies enzymatically catalyzed reactions.

• Gene essentiality data are obtained from the OGEE database and from individual publications.

• BioCyc chemical structures are obtained from multiple sources including ChEBI and PubChem.

• Many literature citations within BioCyc are obtained from PubMed.

• We regularly integrate Gene Ontology annotations from UniProt into BioCyc. These data are combined with internal Gene Ontology terms curated by BioCyc, as follows:
  • If BioCyc 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 BioCyc 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 BioCyc 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.

• Protein feature information from UniProt is periodically loaded into BioCyc. UniProt protein feature data are imported into BioCyc using the following criteria:
  • If the sequence data for the UniProt protein and the BioCyc 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 BioCyc 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.

Third Party Software Tools Integrated into BioCyc

Outside software tools used within the BioCyc website include the following.

• BLAST

• Clustal Omega

• cytoscape.js

• MSAviewer

• PatMatch

• PSortDB

• Pure.css

• SOLR

• Textpresso

• YUI

• ChemAxon