Help:Databases

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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! If you want to do analysis on species closely related to supported species with pathway content, let us know, and we can help come up with an efficient approach.

Current databases are based on Ensembl Release 85 (Jul 2015)
and Ensembl Genomes release 32 (Aug 2016)
Metabolites database have been created from HMDB, Chebi and Wikidata on the 2016-10-12
Interactions database from Rhea release 76 on the 2016-09-27.

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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 and other eukaryotic species
  • Ensembl Genomes for fungi, metazoa, plants, protists and bacterial collections

Small molecule, metabolite databases are generated from the following resources:

The interaction database are generated from the following resource:

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Species By Request

Vertebrates
  • Vicugna pacos (Alpaca)
  • Anolis carolinensis (Anole Lizard)
  • Dasypus novemcinctus (Armadillo)
  • Otolemur garnettii (Bushbaby)
  • Felis catus (Cat)
  • Ciona intestinalis (Ciona intestinalis)
  • Ciona savignyi (Ciona savignyi)
  • Tursiops truncatus (Dolphin)
  • Loxodonta africana (Elephant)
  • Takifugu rubripes (Fugu)
  • Gorilla gorilla (Gorilla)
  • Cavia porcellus (Guinea Pig)
  • Erinaceus europaeus (Hedgehog)
  • Procavia capensis (Hyrax)
  • Dipodomys ordii (Kangaroo rat)
  • Petromyzon marinus (Lamprey)
  • Echinops telfairi (Lesser hedgehog tenrec)
  • Macaca mulatta (Macaque)
  • Oryzias latipes (Medaka)
  • Pteropus vampyrus (Megabat)
  • Myotis lucifugus (Microbat)
  • Microcebus murinus (Mouse Lemur)
  • Monodelphis domestica (Opossum)
  • Pongo pygmaeus (Orangutan)
  • Ochotona princeps (Pika)
  • Ornithorhynchus anatinus (Platypus)
  • Oryctolagus cuniculus (Rabbit)
  • Sorex araneus (Shrew)
  • Choloepus hoffmanni (Sloth)
  • Spermophilus tridecemlineatus (Squirrel)
  • Gasterosteus aculeatus (Stickleback)
  • Tarsius syrichta (Tarsier)
  • Tetraodon nigroviridis (Tetraodon)
  • Tupaia belangeri (Tree Shrew)
  • Taeniopygia guttata (Zebra Finch)
  • all vertebrates
Metazoa

Fungi

Plants

  • Oryza glaberrima (African Rice)
  • Oryza rufipogon (Red Rice)
  • Sorghum bicolor (Sorghum)
  • all plants

Protists

  • Plasmodium falciparum
  • Plasmodium knowlesi
  • Plasmodium vivax
  • all protists

Bacterial Collections

  • Bacillus
  • Escherichia
  • Shigella
  • Mycobacterium
  • Neisseria
  • Pyrococcus
  • Streptococcus
  • all bacteria

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Supported Species

List 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

  • Gibberella zeae (Fusarium)
  • Saccharomyces cerevisiae (Yeast)

Plants

  • Arabidopsis thaliana (Arabidopsis)
  • Glycine max (Soybean)
  • Oryza sativa japonica (Rice)
  • Populus trichocarpa (Poplar)
  • Solanum lycopersicum (Tomato)
  • Vitis vinifera (Wine Grape)

Bacteria

  • Bacillus subtilis (B.subtillis)
  • Clostridium thermocellum
  • Escherichia coli K12 (E.coli)
  • Mycobacterium tuberculosis (Tuberculosis)

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Metabolite Databases

coming soon...


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