WikiPathways Tutorial

For up to date issues or problems with this database please see the wiki.
For more information, please visit WikiPathways.

WIKIpathways was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. The view that NIF has of these data include the name of the pathway, gene and species.

Therefore the way to search these data are either by a pathway name, or by gene name. In the following example, we chose to search for apoptosis.

If the system is allowed to autocomplete for the search term then all of the synonyms of apoptosis are also searched.

Under the Data Type > Pathways tab the information from WikiPathways is brought up. The data include the pathway name, in this case apoptosis and all of the genes that have been annotated to this pathway.

Clicking on the pathway name next to the BIK or CASP genes (both annotated for Rattus novegicus) takes the user to the apoptosis pathway for rat.

Clicking on the image allows a closer examination of the genes and how they are related to one another.

Note this is a wiki site, which is being edited by domain scientists and it frequently changes, especially if there is some dispute in the community about the function of a particular protein. The data that NIF obtains are not the most recent iteration of the pathway; rather they are the ‘curated’ versions of data, i.e., those which have been approved by the WikiPathways staff. This was done intentionally but the user may therefore discover some discrepancies between the NIF and the WIKI view.

For more information, please visit WikiPathways.