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Other Pathway/Genome Databases

Curated Pathway/Genome Databases for many organisms have been created by a variety of institutions and are available from the following Web sites.

In addition to accessing them through the Web, many of these PGDBs can be downloaded to your local copy of Pathway Tools through the PGDB registry described later in this page.

Database Scope Organization
AcypiCyc Acyrthosiphon pisum Universite de Lyon Universite de Lyon
AraCyc Arabidopsis thaliana S. Rhee, Department of Plant Biology, Carnegie Institution, USA
ArthropodaCyc PGDBs for 30 organisms ArthropodaCyc group, France
CalbiCyc Candida albicans Department of Genetics, Stanford U., USA
CottonCyc Gossypium raimondii
Gossypium hirsutum
CottonGen, Washington State University
Gramene Arabidopsis lyrata
Arabidopsis thaliana
Brachypodium distachyon
Chlamydomonas reinhardtii
Cyanidioschyzon merolae
Glycine max
Oryza barthii
Oryza brachyantha
Oryza glaberrima
Oryza minutabb
Oryza minutacc
Oryza nivara
Oryza officinalis
Oryza punctata
Oryza rufipogon
Oryza rufipogon3s
Oryza sativa Nipponbare
 (Japonica rice)
Oryza indica 93-11 (Indica rice)
Physcomitrella patens
Populus trichocarpa
Selaginella moellendorffii
Sorghum bicolor BTX623
Vitis vinifera
Zea mays
Gramene curators (CSHL, OSU, EMBL-EBI)
GutCyc 418 gut bacteria available as flat files only University of British Columbia, Stanford University
MicroScope PGDBs for 3749 Organisms C. Medigue, Genoscope, France
MouseCyc Mus musculus C. Bult, Jackson Laboratory, USA
PlantCyc Arabidopsis thaliana col
Manihot esculenta esculenta
Zea mays mays
Vitis vinifera
Populus trichocarpa
Glycine max
Plant Metabolic Network, Carnegie Institution, USA
PseudoCyc Pseudomonas aeruginosa F. Brinkman, Pseudomonas Genome Project, Simon Fraser U., Canada
SolCyc Solanum lycopersicum
Solanum tuberosum
Solanum melongena
Petunia hybrida
Capsicum anuum
Coffee caniphora
Sol Genomics Network, USA
SoyCyc Glycine max SoyBase
USDA Bacterial Genomes Mannheimia haemolytica Strain USDA-ARS-USMARC-183
Salmonella enterica Subspecies enterica, Strain serovar
Yeast Biochemical Pathways Saccharomyces cerevisiae SGD Curators, Stanford U., USA

Contact us if you'd like your PGDB added to this list.

Registry of Downloadable Pathway/Genome Databases

The PGDB Registry allows users who have installed Pathway Tools locally to easily download PGDBs created by others, or share PGDBs that they have created. Advantages of this approach are that it makes the full power of Pathway Tools available for other PGDBs, and it allows comparative analysis of multiple PGDBs within the same instance of Pathway Tools. [access registry]

Create Your Own Pathway/Genome Database

Interested in creating a pathway/genome DB for your genome? [learn more]