Other Pathway/Genome Databases

Curated Pathway/Genome Databases for many organisms have been created using our Pathway Tools software 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
Aphis glycines
Daktulosphaira vitifoliae
Diuraphis noxia
Myzus cerasi
Myzus persicase
Rhoplalossiphum padi
Universite de Lyon
ArthropodaCyc PGDBs for 32 arthropods ArthropodaCyc group, France
CacaoCyc Theobroma Cacao MARS, USDA-ARS, IBM,NCGR, Clemson U., HudsonAlpha Institute, Indiana U., Washington State U.
CottonCyc Gossypium raimondii
Gossypium hirsutum
Gossypium arboreum
Gossypium barbadense
Gossypium turneri
CottonGen, Washington State University
Gramene Brachypodium distachyon
Oryza sativa Nipponbare
 (Japonica rice)
Sorghum bicolor BTX623
Zea mays
and mirrored PGDBs for 9 organisms
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
Nannocyc PGDBs for 3 Nannochloropsis species Single Cell Center, Qingdao Institute of Bioenergy and Bioprocess Technology
PlantCyc PGDBs for 101 plants Plant Metabolic Network, Carnegie Institution, USA
PseudoCyc Pseudomonas aeruginosa F. Brinkman, Pseudomonas Genome Project, Simon Fraser U., Canada
SoyCyc Glycine max SoyBase
Trypanocyc Trypanosoma brucei
Leishmania major
INRA Toulouse, France
USDA Bacterial Genomes Mannheimia haemolytica Strain USDA-ARS-USMARC-183
Salmonella enterica Strain serovar Montevideo str. CDC 2012K-1544
VitisCyc and others Vitis vinifera
Eucalyptus grandis
Fragaria vesca
and mirrored PGDBs for 10 organisms
Center for Genome Research and Biocomputing, Oregon State University
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]