Download Pathways

From WikiPathways

Revision as of 22:49, 24 September 2020

Versioned Releases

Each month we release an updated set of pathways in various data and image formats. These pathways have been reviewed and tagged as approved, and are considered ready for analysis and data overlays.

Current version: 20200810 (10 August 2020)

Vertebrates

• Bos taurus
• Canis familiaris
• Danio rerio
• Equus caballus
• Gallus gallus
• Homo sapiens
• Mus musculus
• Pan troglodytes
• Rattus norvegicus
• Sus scrofa

Invertebrates

• Anopheles gambiae
• Caenorhabditis elegans
• Drosophila melanogaster

Plants

• Arabidopsis thaliana
• Hordeum vulgare
• Oryza sativa
• Populus trichocarpa
• Solanum lycopersicum
• Zea mays

Eukaryotic microorganisms

• Gibberella zeae
• Saccharomyces cerevisiae
• Plasmodium falciparum

Bacteria

• Bacillus subtilis
• E.coli
• Mycobacterium tuberculosis

Programmatic Access

The archive of current and past collections of pathways in various formats at data.wikipathways.org is accessible programmatically as well. Depending on your preferences, there are many ways to identify and download the collection you need.

Note: Our files contain the date of creation in their names so that you can be sure which collection your are using and to avoid overwriting local copies of these files.

1. rWikiPathways is an R package that provides an helper function called downloadPathwayArchive that will retrieve the latest file for you per species and format, e.g.,

   downloadPathwayArchive(organism="Mus musculus”, format=‘gmt’)

2. Filename pattern allows you to infer the filename of the latest collection given the current date. For example, since we always release our archive collections on the 10th of each month, you know that the latest filename is the nearest prior date matching that pattern, e.g., 20180910 would be the current file from Sep 10 to Oct 10, 2018. Caution: this might break if for some unforeseen reason we are unable to produce the archive on schedule.
3. Bash scripting allows you to scrape the currently available filenames and guarantee that you are getting the latest file no matter what the name might be. Here is an example of a one-liner to get a list of all the current GMT files:

   echo "cat //html/body/div/table/tbody/tr/td/a" |  xmllint --html --shell http://data.wikipathways.org/current/gmt/ | grep -o -E ">(.*gmt)<" | sed -E 's/(<|>)//g'

   And here is a version that would return the latest GMT for mouse:

   echo "cat //html/body/div/table/tbody/tr/td/a" |  xmllint --html --shell http://data.wikipathways.org/current/gmt/ | grep -o -E ">.*Mus_musculus.gmt<" | sed -E 's/(<|>)//g'

Other Collections