Template:Interactive pathway maps/doc

This template is the product of a custom export process of WikiPathways content as interactive pathway maps for Wikipedia articles. Please do not edit these templates directly as they include calculated hyperlinks and annotations based on original content curated at WikiPathways. Please feel free to edit and update the pathway content at WikiPathways. Your changes will be reflected here when the template is regenerated.

The collaborative design of this template, which is actually a set of nested templates with an image map at the core, was initially proposed and refined in collaboration with Gene Wiki and MCB. Please review the background of this discussion before making edits. Feel free to make suggestions in the associated talk pages.

The process of generating the content using this template involves a combination of scripts and manual steps detailed at https://github.com/wikipathways/Wikipedia-template. Feel free to contact WikiPathways if you need assistance updating or creating content using this template.

Features

• Gene links – click on blue-underlined gene boxes in pathway to go to the corresponding Gene Wiki article
• Metabolite links – click on blue-underlined metabolite boxes in pathway to go to the corresponding metabolite article
• Start new pages – click on red-underlined boxes to start a new Wikipedia article where one currently does not exist
• Bold self links – the gene or metabolite focused on in the current article is displayed as a bold-bordered self link
• Pathway links – click anywhere in the background on the pathway to go to the corresponding pathway article with an expanded view of the interactive pathway map
• Variable-controlled cropped view – pathway maps can be cropped by referencing a gene or metabolite (see Usages #2 and #3 below).
• Variable-controlled scroll view – pathway maps can be viewed in a scrollable window at a particular width and height (see Usage #4 below).

Parameters

• |header= — Box heading text.

Usage

This template is commonly transcluded into the following types of articles in the following ways:

Pathway articles

Where you want to see the full pathway

{{TCACycle WP78}}

Gene Wiki articles

Where you want to crop the pathway view to center on a particular gene

{{TCACycle WP78|highlight=Dihydrolipoyl_transacetylase}}

Metabolite articles

Where you want to crop the pathway view to center on a particular metabolite

{{TCACycle WP78|highlight=Fumaric_acid}}

Miscellaneous

Where you override default views and specify the width and height of a scrollable window in which to view the entire pathway

{{TCACycle WP78|width=600|height=300}}

• width: the width of the scrollable window
• height: the height of the scrollable window

PLEASE DO NOT

Please do not transclude below the References section or into other templates commonly transcluded below the Reference section. This produces a red warning (missing refs tag) due to the use of in-line references. Thank you!

Examples

• Citric acid cycle pathway ({{TCACycle WP78}})
• DLAT gene wiki article ({{GlycolysisGluconeogenesis_WP534}})
• Where is this template used?

Known issues

• When there is more than one copy of a gene or metabolite on a pathway, clicking on any copy will lead to the same page (as expected) and to the same highlighted and centered view (which may or may not be the particular copy you clicked on). This is because the highlighting and centering are determined by the variable passed in to the template and not by what exactly you click on. So, when using this template on a gene or metabolite article, take note of which copy (if there is more than one) is being highlighted in the view. The template knows about the other copies and you can choose which is the best representative copy to highlight by passing in the right variable. The first copy is given the name of the article (e.g., Apple_acid); additional copies are named "alt1", "alt2", etc. (e.g., Apple_acid__alt1). Note the two underscore characters between the name and the "alt" designation. In this way you can preview and decide which copy you want to highlight on a given gene or metabolite article.
• We do not have a public way of exporting pathways yet.