Every page of the Endonet web interface has its own paragraph with sub-paragraphs for important options. Throughout the pages, you will find symbols, which will redirect you to the corresponding section of this help page when clicked.

The "search" page

Here you can search for items, select predefined sets, or browse the hormone classification.

Search for

Please enter your term(s) of interest (hormone and/or receptor and/or tissue) in the corresponding field(s). Asterisks are allowed as wildcards. When hitting the "Go" button, the database gets queried for objects matching the pattern(s) you've entered. Only one search pattern is allowed for each field, but you can easily combine several queries to a query set (see below).
For tissues the search engine uses the Cytomer ontology as additional backend for searching names and synonyms.

Predefined sets

Some well-established endocrine pathways are offered in the form of "predefined sets". When selected, such sets can be used for obtaining a quick overview or as a starting point for more complex queries. You can also freely combine the predefined sets with individual queries.

Browse the data

Instead of searching for a name of a hormone, you can also browse the hierarchical hormone classification featured by EndoNet.

The "search results" page

On this page, the results of your queries or selections are displayed. Each item is linked to a page offering more details.

Add items to your set

Look through your search results and deselect all false hits. To prepare items for visualization, click the "add items to your set" button. The result will appear in the "Sets / query set" page.

The "query sets" page

This page is divided into two parts. In the upper part, you can select several options, whereas in the lower part the items of your current query set are listed.

By hitting the "next search" button, a new query can be performed and combined with the current one. This procedure may be repeated as many times as required, thus allowing to add all items of interest to a common query set. Finally, the set can be used further to reconstruct and visualize a network. Items can be removed by clicking the corresponding red cross icon. All items can be removed in one step by clicking "reset query". To display a graph, click on "display graph". However, before starting graph visualization, you may want to adjust some of the following parameters:

Show transport media

On demand, the hormones' transport media may be included in the visualization of intercellular edges by selecting this option. The media will be included as extra nodes while the rest of the graph remains unchanged.

Steps downstream and upstream

The maximum number of steps can be selected separately for the upstream and downstream part of the network reconstruction process. Please keep in mind that large numbers may increase the complexity of the result graph dramatically! (A step is defined as a hormone-receptor interaction.)

Highlight search items

The option "highlight search item" will render the items initially searched for in a bright reddish color when checked. For more details, please consult the figure legend.

Graph layout flow

The graph may be displayed either in a "top to down" or in a "left to right" layout, according to your preferences. By default, the graph will grow horizontally; however, you might find it easier to scroll the result image vertically.

Show all hormones and/or receptors

By default, only those hormones and receptors are shown, which the reconstruction algorithm actually comes across when building the network. To show all hormones and/or receptors for a tissue, select the corresponding options, i. e. "show all hormones for a tissue" and/or "show all receptors for a tissue".

Graphics format

The graph is available in two different grafics formats: PNG and SVG. While virtually every browser supports PNG (a "pixel" or "bitmap" format), only a few of them provide a zoom functionality for bitmap pictures. SVG, on the other hand, provides more functionality (including perfect image quality throughout all zoom factors), but until now most browsers don't support SVG natively and require an SVG plugin for displaying this vector-based format.

Konqueror
supports SVG natively.

Opera 8.0 or newer
supports SVG natively; however, if some graphics elements overlap one another, only the underlaying element is clickable.

Mozilla Firefox 1.5 Beta 2
supports SVG natively, but in the beta version the zoom functionality is still missing.

All other browsers we've tested so far (Internet Explorer, Mozilla, Firefox < 1.5 etc.) will require you to download a suitable plugin, e.g. Adobe's SVG plugin.

SVG Viewer Plugin Download

Current version: http://www.adobe.com/svg/viewer/install/main.html
Old versions: http://www.adobe.com/svg/viewer/install/old.html

The Adobe SVG plugin
Please install this plugin if your browser doesn't have built-in support for SVG. It offers the functionality to zoom into the picture by clicking with the mouse while pressing <Crtl> or <Ctrl>+<Shift>. If you still cannot display SVG in Mozilla Firefox after installing the plugin, you probalbly have to manually copy a library file from the plugin's installation directory to your browser's plugin directory (which is located below the browser's installation directory). The library file is called NPSVG3.dll on Windows and libNPSVG3.so on Linux.

The "graph" page

From the selected items, a bipartite graph is built and visualized according to your options. By clicking on an entity, such as a hormone, a receptor or a tissue, you will be directed to the corresponding detail page. If you have chosen SVG as your output format, the interaction edges will be highlighted if you point at them with your mouse cursor, and -- depending on the capabilities of your browser/plugin -- you will also have zoom functionality (see above). Additional information about the item under your mouse pointer will be shown in a tooltip.

EndoNet::help