Download Pathways
From WikiPathways
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Choose one of the file types below to download a set of pathways in that format. Choose between the following sets:
- Analysis collection pathways
- Only pathways that have been explicitly marked with the 'Analysis collection' curation tag. This includes pathways that have been carefully curated and typically excludes draft or test pathways not intended for distribution. (recommended)
- All pathways
- Includes non-featured pathways, but still excludes test or tutorial pathways (such as the Sandbox pathway).
GPML
Click on one of the links below to download all pathways in GPML format. You can view and edit GPML files in PathVisio. From PathVisio you can also export these files to the [www.genmapp.org GenMAPP] mapp format and PDF.
KEGG pathways for select species are available in GPML format at PathVisio.org. (KEGG content current as of September 14th, 2010)
BioPAX
Click on one of the links below to download all pathways in BioPAX level 3 format.
Eu.Gene
Click on one of the links below to download all pathways in the Eu.Gene format (pwf). Eu.Gene is a tool for microarray analysis in context of biological pathways (read more).
Plain text
Click on one of the links below to download all pathways in plain text format. This format contains a list of all datanodes, with the identifier in the first column, and the database system in the second column.
Click on one of the links below to download all pathways in Portable Document Format (PDF).
SVG
Click on one of the links below to download all pathways in SVG format. The SVG files can be used to create high quality images for publication purposes. You can edit and convert the SVG files using Inkscape.
PNG
Click on one of the links below to download all pathways in the Portable Network Graphics (png) format.
Flatfile
Click on one of the links below to download all pathways in either a tab-delimited or HTML table format. The output includes gene, protein and small molecule contents. You can choose between "original" and "mapped" versions, which refer to whether only the original identifiers are provided or if you want them mapped to all available identifier systems.
- Anopheles gambiae (original: tab, html) (mapped: tab, html)
- Arabidopsis thaliana (original: tab, html) (mapped: tab, html)
- Bos taurus (original: tab, html) (mapped: tab, html)
- Bacillus subtilis (original: tab, html) (mapped: tab, html)
- Caenorhabditis elegans (original: tab, html) (mapped: tab, html)
- Canis familiaris (original: tab, html) (mapped: tab, html)
- Danio rerio (original: tab, html) (mapped: tab, html)
- Drosophila melanogaster (original: tab, html) (mapped: tab, html)
- Equus caballus (original: tab, html) (mapped: tab, html)
- Gallus gallus (original: tab, html) (mapped: tab, html)
- Homo sapiens (original: tab, html) (mapped: tab, html)
- Mus Musculus (original: tab, html) (mapped: tab, html)
- Mycobacterium tuberculosis (original: tab, html) (mapped: tab, html)
- Oryza sativa (original: tab, html) (mapped: tab, html)
- Pan troglodytes (original: tab, html) (mapped: tab, html)
- Rattus norvegicus (original: tab, html) (mapped: tab, html)
- Saccharomyces cerevisiae (original: tab, html) (mapped: tab, html)
- Sus scrofa (original: tab, html) (mapped: tab, html)
- Zea mays (original: tab, html) (mapped: tab, html)
