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
- Ensembl Genomes for plants and bacterial collections
Small molecule, metabolite databases are generated from the following resources:
Species By Request
Vertebrates
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Metazoa Fungi | Plants
Protists
Bacterial Collections
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Supported Species
Vertebrates
- Bos taurus (Cow)
- Canis familiaris (Dog)
- Danio rerio (Zebrafish)
- Equus caballus (Horse)
- Gallus gallus (Chicken)
- Homo sapiens (Human)
- Mus musculus (Mouse)
- Pan troglodytes (Chimpanzee)
- Rattus norvegicus (Rat)
- Sus scrofa (Pig)
- Xenopus tropicalis (Frog)
Metazoa
- Anopheles gambiae (Mosquito)
- Caenorhabditis elegans (C.elegans)
- Drosophila melanogaster (Fruit fly)
Fungi
- Saccharomyces cerevisiae (Yeast)
Plants
- Arabidopsis thaliana (Arabidopsis)
- Oryza sativa japonica (Rice)
- Populus trichocarpa (Poplar)
Bacteria
- Bacillus subtilis (B.subtillis)
- Escherichia coli K12 (E.coli)
- Mycobacterium tuberculosis (Tuberculosis)
