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 USDA SciNet

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

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]

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