Help:Databases
From WikiPathways
WikiPathways Databases
The backbone of WikiPathways is made up of databases. The gene, protein and metabolite databases supporting pathway objects provide connections to well defined and annotated biological entities. The databases of WikiPathways derive from the BridgeDb system as Java-embedded Derby databases. BridgeDb is an ID mapping framework for bioinformatics applications.
To the right, you'll find the current list of supported species at WikiPathways. Below, you'll learn about the resources used to build the databases and the potential for additional species support by request.
If you have a favorite species of interest for a pathway curation effort, let us know!
Resources
Gene and protein databases are built in sync with Ensembl's build releases. The BridgeDb system can generate Derby database for WikiPathways from any "ensemblized" genome database. Our current sources include:
- Ensembl for vertebrates, metazoa and fungi
- Gramene for plant species
- Ensembl Genomes for bacterial collections
Small molecule, metabolite databases are generated from the following resources:
Species By Request
Animals
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| Plants
Protists
Bacterial Collections
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Supported Species
Animals
- Anopheles gambiae (Mosquito)
- Caenorhabditis elegans (C.elegans)
- Gallus gallus (Chicken)
- Pan troglodytes (Chimpanzee)
- Bos taurus (Cow)
- Canis familiaris (Dog)
- Drosophila melanogaster (Fruit fly)
- Equus caballus (Horse)
- Homo sapiens (Human)
- Mus musculus (Mouse)
- Rattus norvegicus (Rat)
- Xenopus tropicalis (Western clawed frog)
- Danio rerio (Zebrafish)
Fungi
- Saccharomyces cerevisiae (Budding yeast)
Plants
- Arabidopsis thaliana (Arabidopsis)
- Oryza sativa japonica (Rice)
- Populus trichocarpa (Western Balsam Poplar)
Bacteria
- Bacillus subtilis (B.subtillis)
- Escherichia coli K12 (E.coli)
