BioCyc is a collection of Pathway Genome Databases (PGDBs) containing genomic and metabolic pathway data on many organisms. We are very excited to now offer this subscription database to current Penn faculty, staff and students.

Manuel de la Cruz Gutiérrez, PhD (dmanuel@upenn.edu) and Subin George (sgeo@upenn.edu) will be offering the first BioCyc workshop on March 12, 2019 at noon.  If interested please register here!

BioCyc databases are comprised of curated data from publications enabling researchers to easily integrate these data into their research. In addition, BioCyc provides tools for database searching and visualization, omics data analysis, and comparative analysis. BioCyc also integrates information such as protein feature/Gene Ontology from other bioinformatics databases.

BioCyc databases are organized into three tiers as follows:

Tier 1 PGDBs are constantly updated and consist of:

• EcoCyc (consists of gene, metabolite, and pathway data on E.coli; visualization tools such as genome browser are also provided)
• HumanCyc (collection of human gene and metabolic pathway data)
• MetaCyc (provides a comprehensive list of experimentally derived metabolic pathways and enzymes from more than 2500 organisms)
• AraCyc (Arabidopsis thaliana; model organism)
• LeishCyc (Leishmania major)
• YeastCyc (Saccharomyces cerevisiae; model organism).

Tier2 PGDBs are computationally generated and are updated moderately, and include model organisms such as drosophila melanogaster and mus musculus.

Tier3 PGDBs are also computationally generated but are not updated or reviewed.

View the full list of PGDBs.

More information about BioCyc.

Register for the first BioCyc workshop on March 12, 2019 at noon!