KGML-ED allows the user to not only navigate (in-place) from one pathway to another, but also to load several pathways (or pathway files) in one step. This is described in the next section of this tutorial.

Often multiple pathways or even single pathways contain more than one entry of the same ID, mostly to improve the layout of the pathway. Such duplicated entries may be merged into a single entity as described at the end of this tutorial.

 

KGML-ED supports the loading of several pathways into a single view. This may be achieved, by selecting several files in the File-Open dialog at once or by selecting several pathway items in the “Load” side panel. You may also select a category in the “Load” panel, to load all pathways, connected to that category item in the tree. The number of pathways, belonging to one group is shown in parenthesis. You may use the “Search” field in at the bottom of this panel, to limit the number of relevant pathways.

 

A example: You could select all “mammal” organisms (use the search field when selecting the organisms), and load the pathway overview for all of these organisms at once. Then you could search for “TCA” in the side panel, and select the top (root) node. By clicking the button “Load selected pathways”, all TCA pathways of mammal organisms would be loaded into a single view, making it easy to locate differences between the pathways from different organisms.

 

When loading multiple pathways in one step, a option dialog is shown. It contains three settings:

 

(1) The option to load each pathway in a separate window, or into a single view. If this option is enabled, settings (2) and (3) are considered:

(2) The option to modify the grid-layout, which is used to place multiple pathways in one view. It is possible to specify the maximum number of pathways, which are placed next to each other. If the maximum is reached, a new “row” for the placement of a pathway starts.

(3) The option to process defined map-links between the loaded pathways. If this option is selected, after loading all pathways map-links, pointing to a loaded pathway are “resolved”. This means, a reference link to the particular pathway element in the referenced pathway is made. Map-link nodes of loaded pathways are thus removed. Another implication of this processing is, that multiple map-links to the same (not yet loaded) pathway are merged into a single map-link.

 

A example: By selecting the pathway group “1.3 Lipid Metabolism” and clicking the “Load Selected Pathways” button, all 13 pathways of that group will be placed into a single view and map-links pointing to another pathway of that group will be resolved, creating a unified view of that pathway category in a single step. Remark: Sometimes a warning message about a “not unique reaction” will be shown. This means, that a reaction is defined as reversible in one pathway and irreversible in another. In order to create a “truly integrated” pathway, you could consider to merge multiple occurrences of compounds, found in several pathways. This is described at the end of this tutorial.

 

Use the command “Find duplicate entries” (tab “Process) to locate multiple entries, which have the same ID. The command considers the current selection, if a node selection is active. For example you may first select all compounds, and then use this command to limit the selection to all compounds which appear more than once in the view.

It is very common that entries appear multiple times in a pathway. This is most apparent for enzymes, but also compounds may be sometimes more than once shown in a pathway. A common reason for that is, that the pathway layout is improved, as less edges need to be drawn from one end of the pathway to the other (the result are less edge crossings).

In some situations it would for example be interesting, to easily see all connections from one entry (be it one enzyme, compound or map-link) to other nodes. In case this entry is shown several times in the pathway view, this is not as easy, as in the case, that no duplicate entries are shown.

To merge multiple entries, use the command “Condense into single entities” (tab “Process”). When performing this command, a settings dialog will be shown. The first setting is “Limit scope to Node-Selection”, if this is enabled, only entries, related to the current selection will be processed. The second option is “Limit Scope to Selected Entry-Type”, if this is enabled, the command works only on duplicate entries of the specified type (e.g. “compound”). Both settings are independent, so if you for example select a particular pathway (“Edit/Select Pathway-Subgraph”), and limit the scope to “compound”, only multiple identical compounds of that pathway would be merged.