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.
CalbiCyc	Candida albicans	Department of Genetics, Stanford U., USA
Cathacyc	Catharanthus roseus	European Union Seventh Framework Programme, European Molecular Biology Organization and the European Commission support.
CottonCyc	Gossypium raimondii Gossypium hirsutum Gossypium arboreum Gossypium barbadense Gossypium turneri	CottonGen, Washington State University
DiatomCyc	Phaeodactylum tricornutum	Center for Plant Systems Biology, University of Ghent, Belgium
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
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]

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